9QM5 | pdb_00009qm5

Krypton-pressurized Methyl-Coenzyme M reductase of an ANME-2c isolated from a microbial enrichment

PDB DOI: https://doi.org/10.2210/pdb9QM5/pdb

Classification: TRANSFERASE
Organism(s): Candidatus Methanogasteraceae archaeon
Mutation(s): No

Deposited: 2025-03-21 Released: 2025-07-16
Deposition Author(s): Mueller, M.-C., Wagner, T.
Funding Organization(s): European Research Council (ERC), German Research Foundation (DFG), Netherlands Organisation for Scientific Research (NWO), Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.155 (Depositor), 0.154 (DCC)
R-Value Work:
0.129 (Depositor), 0.128 (DCC)
R-Value Observed:
0.131 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Atomic resolution structures of key enzyme MCR in anaerobic methanotrophy reveal novel and extensive post-translational modifications.

Mueller, M.-C., Wissink, M., Mukherjee, P., Von Possel, N., Laso-Perez, R., Engilberge, S., Carpentier, P., Kahnt, J., Wegener, G., Welte, C.U., Wagner, T.

To be published.

Macromolecule Content

Total Structure Weight: 562.75 kDa
Atom Count: 43,317
Modeled Residue Count: 5,020
Deposited Residue Count: 5,040
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c	A, D, G, J	561	Candidatus Methanogasteraceae archaeon	Mutation(s): 0 EC: 2.8.4.1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta subunit of the Methyl-coenzyme M reductase from ANME-2c	B, E, H, K	434	Candidatus Methanogasteraceae archaeon	Mutation(s): 0 EC: 2.8.4.1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c	C, F, I, L	265	Candidatus Methanogasteraceae archaeon	Mutation(s): 0 EC: 2.8.4.1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 12 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F43 (Subject of Investigation/LOI) Query on F43 Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth D] SDF format, chain FC [auth G] SDF format, chain ZC [auth J] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth D] MOL2 format, chain FC [auth G] MOL2 format, chain ZC [auth J] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth D] mmCIF format, chain FC [auth G] mmCIF format, chain ZC [auth J]	AA [auth A], AB [auth D], FC [auth G], ZC [auth J]	FACTOR 430 C₄₂ H₅₁ N₆ Ni O₁₃ XLFIRMYGVLUNOY-SXMZNAGASA-M		Interactions Focus chain AA [auth A] Focus chain AB [auth D] Focus chain FC [auth G] Focus chain ZC [auth J] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth D] Focus chain FC [auth G] Focus chain ZC [auth J]
TP7 (Subject of Investigation/LOI) Query on TP7 Download Ideal Coordinates CCD File SDF format, chain AC [auth G] SDF format, chain AD [auth J] SDF format, chain YA [auth D] SDF format, chain Z [auth A] MOL2 format, chain AC [auth G] MOL2 format, chain AD [auth J] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth A] mmCIF format, chain AC [auth G] mmCIF format, chain AD [auth J] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth A]	AC [auth G], AD [auth J], YA [auth D], Z [auth A]	Coenzyme B C₁₁ H₂₂ N O₇ P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N		Interactions Focus chain AC [auth G] Focus chain AD [auth J] Focus chain YA [auth D] Focus chain Z [auth A] Interactions & Density Focus chain AC [auth G] Focus chain AD [auth J] Focus chain YA [auth D] Focus chain Z [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain BB [auth D] SDF format, chain EC [auth G] SDF format, chain JC [auth H] SDF format, chain W [auth A] SDF format, chain WB [auth G] SDF format, chain XA [auth D] MOL2 format, chain BB [auth D] MOL2 format, chain EC [auth G] MOL2 format, chain JC [auth H] MOL2 format, chain W [auth A] MOL2 format, chain WB [auth G] MOL2 format, chain XA [auth D] mmCIF format, chain BB [auth D] mmCIF format, chain EC [auth G] mmCIF format, chain JC [auth H] mmCIF format, chain W [auth A] mmCIF format, chain WB [auth G] mmCIF format, chain XA [auth D]	BB [auth D] EC [auth G] JC [auth H] W [auth A] WB [auth G] BB [auth D], EC [auth G], JC [auth H], W [auth A], WB [auth G], XA [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain BB [auth D] Focus chain EC [auth G] Focus chain JC [auth H] Focus chain W [auth A] Focus chain WB [auth G] Focus chain XA [auth D] Interactions & Density Focus chain BB [auth D] Focus chain EC [auth G] Focus chain JC [auth H] Focus chain W [auth A] Focus chain WB [auth G] Focus chain XA [auth D]
COM (Subject of Investigation/LOI) Query on COM Download Ideal Coordinates CCD File SDF format, chain BD [auth J] SDF format, chain FA [auth A] SDF format, chain ZA [auth D] SDF format, chain ZB [auth G] MOL2 format, chain BD [auth J] MOL2 format, chain FA [auth A] MOL2 format, chain ZA [auth D] MOL2 format, chain ZB [auth G] mmCIF format, chain BD [auth J] mmCIF format, chain FA [auth A] mmCIF format, chain ZA [auth D] mmCIF format, chain ZB [auth G]	BD [auth J], FA [auth A], ZA [auth D], ZB [auth G]	1-THIOETHANESULFONIC ACID C₂ H₆ O₃ S₂ ZNEWHQLOPFWXOF-UHFFFAOYSA-N		Interactions Focus chain BD [auth J] Focus chain FA [auth A] Focus chain ZA [auth D] Focus chain ZB [auth G] Interactions & Density Focus chain BD [auth J] Focus chain FA [auth A] Focus chain ZA [auth D] Focus chain ZB [auth G]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain BC [auth G] SDF format, chain CC [auth G] SDF format, chain FB [auth D] SDF format, chain IB [auth E] SDF format, chain IC [auth H] SDF format, chain LD [auth K] SDF format, chain RD [auth L] SDF format, chain XC [auth J] SDF format, chain YC [auth J] MOL2 format, chain BA [auth A] MOL2 format, chain BC [auth G] MOL2 format, chain CC [auth G] MOL2 format, chain FB [auth D] MOL2 format, chain IB [auth E] MOL2 format, chain IC [auth H] MOL2 format, chain LD [auth K] MOL2 format, chain RD [auth L] MOL2 format, chain XC [auth J] MOL2 format, chain YC [auth J] mmCIF format, chain BA [auth A] mmCIF format, chain BC [auth G] mmCIF format, chain CC [auth G] mmCIF format, chain FB [auth D] mmCIF format, chain IB [auth E] mmCIF format, chain IC [auth H] mmCIF format, chain LD [auth K] mmCIF format, chain RD [auth L] mmCIF format, chain XC [auth J] mmCIF format, chain YC [auth J]	BA [auth A] BC [auth G] CC [auth G] FB [auth D] IB [auth E] BA [auth A], BC [auth G], CC [auth G], FB [auth D], IB [auth E], IC [auth H], LD [auth K], RD [auth L], XC [auth J], YC [auth J]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain BC [auth G] Focus chain CC [auth G] Focus chain FB [auth D] Focus chain IB [auth E] Focus chain IC [auth H] Focus chain LD [auth K] Focus chain RD [auth L] Focus chain XC [auth J] Focus chain YC [auth J] Interactions & Density Focus chain BA [auth A] Focus chain BC [auth G] Focus chain CC [auth G] Focus chain FB [auth D] Focus chain IB [auth E] Focus chain IC [auth H] Focus chain LD [auth K] Focus chain RD [auth L] Focus chain XC [auth J] Focus chain YC [auth J]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CD [auth J] SDF format, chain DD [auth J] SDF format, chain EA [auth A] SDF format, chain ED [auth J] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain WA [auth D] MOL2 format, chain CD [auth J] MOL2 format, chain DD [auth J] MOL2 format, chain EA [auth A] MOL2 format, chain ED [auth J] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain WA [auth D] mmCIF format, chain CD [auth J] mmCIF format, chain DD [auth J] mmCIF format, chain EA [auth A] mmCIF format, chain ED [auth J] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain WA [auth D]	CD [auth J] DD [auth J] EA [auth A] ED [auth J] MA [auth C] CD [auth J], DD [auth J], EA [auth A], ED [auth J], MA [auth C], NA [auth C], WA [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CD [auth J] Focus chain DD [auth J] Focus chain EA [auth A] Focus chain ED [auth J] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain WA [auth D] Interactions & Density Focus chain CD [auth J] Focus chain DD [auth J] Focus chain EA [auth A] Focus chain ED [auth J] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain WA [auth D]
KR (Subject of Investigation/LOI) Query on KR Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain GB [auth E] SDF format, chain GC [auth H] SDF format, chain ID [auth K] SDF format, chain JA [auth C] SDF format, chain JB [auth F] SDF format, chain KB [auth F] SDF format, chain KC [auth I] SDF format, chain LC [auth I] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain ND [auth L] SDF format, chain O [auth A] SDF format, chain OB [auth G] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain PB [auth G] SDF format, chain PC [auth J] SDF format, chain Q [auth A] SDF format, chain QA [auth D] SDF format, chain QB [auth G] SDF format, chain QC [auth J] SDF format, chain R [auth A] SDF format, chain RA [auth D] SDF format, chain RB [auth G] SDF format, chain RC [auth J] SDF format, chain S [auth A] SDF format, chain SA [auth D] SDF format, chain SB [auth G] SDF format, chain SC [auth J] SDF format, chain T [auth A] SDF format, chain TA [auth D] SDF format, chain TB [auth G] SDF format, chain TC [auth J] SDF format, chain UA [auth D] SDF format, chain UB [auth G] SDF format, chain UC [auth J] SDF format, chain VC [auth J] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth E] MOL2 format, chain GC [auth H] MOL2 format, chain ID [auth K] MOL2 format, chain JA [auth C] MOL2 format, chain JB [auth F] MOL2 format, chain KB [auth F] MOL2 format, chain KC [auth I] MOL2 format, chain LC [auth I] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain ND [auth L] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth G] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain PB [auth G] MOL2 format, chain PC [auth J] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain QB [auth G] MOL2 format, chain QC [auth J] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain RB [auth G] MOL2 format, chain RC [auth J] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain SB [auth G] MOL2 format, chain SC [auth J] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth D] MOL2 format, chain TB [auth G] MOL2 format, chain TC [auth J] MOL2 format, chain UA [auth D] MOL2 format, chain UB [auth G] MOL2 format, chain UC [auth J] MOL2 format, chain VC [auth J] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth E] mmCIF format, chain GC [auth H] mmCIF format, chain ID [auth K] mmCIF format, chain JA [auth C] mmCIF format, chain JB [auth F] mmCIF format, chain KB [auth F] mmCIF format, chain KC [auth I] mmCIF format, chain LC [auth I] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain ND [auth L] mmCIF format, chain O [auth A] mmCIF format, chain OB [auth G] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain PB [auth G] mmCIF format, chain PC [auth J] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain QB [auth G] mmCIF format, chain QC [auth J] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain RB [auth G] mmCIF format, chain RC [auth J] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth D] mmCIF format, chain SB [auth G] mmCIF format, chain SC [auth J] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth D] mmCIF format, chain TB [auth G] mmCIF format, chain TC [auth J] mmCIF format, chain UA [auth D] mmCIF format, chain UB [auth G] mmCIF format, chain UC [auth J] mmCIF format, chain VC [auth J]	GA [auth B] GB [auth E] GC [auth H] ID [auth K] JA [auth C] GA [auth B], GB [auth E], GC [auth H], ID [auth K], JA [auth C], JB [auth F], KB [auth F], KC [auth I], LC [auth I], M [auth A], N [auth A], ND [auth L], O [auth A], OB [auth G], P [auth A], PA [auth D], PB [auth G], PC [auth J], Q [auth A], QA [auth D], QB [auth G], QC [auth J], R [auth A], RA [auth D], RB [auth G], RC [auth J], S [auth A], SA [auth D], SB [auth G], SC [auth J], T [auth A], TA [auth D], TB [auth G], TC [auth J], UA [auth D], UB [auth G], UC [auth J], VC [auth J]	KRYPTON Kr DNNSSWSSYDEUBZ-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain GB [auth E] Focus chain GC [auth H] Focus chain ID [auth K] Focus chain JA [auth C] Focus chain JB [auth F] Focus chain KB [auth F] Focus chain KC [auth I] Focus chain LC [auth I] Focus chain M [auth A] Focus chain N [auth A] Focus chain ND [auth L] Focus chain O [auth A] Focus chain OB [auth G] Focus chain P [auth A] Focus chain PA [auth D] Focus chain PB [auth G] Focus chain PC [auth J] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain QB [auth G] Focus chain QC [auth J] Focus chain R [auth A] Focus chain RA [auth D] Focus chain RB [auth G] Focus chain RC [auth J] Focus chain S [auth A] Focus chain SA [auth D] Focus chain SB [auth G] Focus chain SC [auth J] Focus chain T [auth A] Focus chain TA [auth D] Focus chain TB [auth G] Focus chain TC [auth J] Focus chain UA [auth D] Focus chain UB [auth G] Focus chain UC [auth J] Focus chain VC [auth J] Interactions & Density Focus chain GA [auth B] Focus chain GB [auth E] Focus chain GC [auth H] Focus chain ID [auth K] Focus chain JA [auth C] Focus chain JB [auth F] Focus chain KB [auth F] Focus chain KC [auth I] Focus chain LC [auth I] Focus chain M [auth A] Focus chain N [auth A] Focus chain ND [auth L] Focus chain O [auth A] Focus chain OB [auth G] Focus chain P [auth A] Focus chain PA [auth D] Focus chain PB [auth G] Focus chain PC [auth J] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain QB [auth G] Focus chain QC [auth J] Focus chain R [auth A] Focus chain RA [auth D] Focus chain RB [auth G] Focus chain RC [auth J] Focus chain S [auth A] Focus chain SA [auth D] Focus chain SB [auth G] Focus chain SC [auth J] Focus chain T [auth A] Focus chain TA [auth D] Focus chain TB [auth G] Focus chain TC [auth J] Focus chain UA [auth D] Focus chain UB [auth G] Focus chain UC [auth J] Focus chain VC [auth J]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain CB [auth D] SDF format, chain DA [auth A] SDF format, chain DB [auth D] SDF format, chain DC [auth G] SDF format, chain EB [auth D] SDF format, chain FD [auth J] SDF format, chain GD [auth J] SDF format, chain HD [auth J] SDF format, chain IA [auth B] SDF format, chain MB [auth F] SDF format, chain MD [auth K] SDF format, chain NC [auth I] SDF format, chain OC [auth I] SDF format, chain QD [auth L] SDF format, chain X [auth A] SDF format, chain XB [auth G] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth D] MOL2 format, chain DC [auth G] MOL2 format, chain EB [auth D] MOL2 format, chain FD [auth J] MOL2 format, chain GD [auth J] MOL2 format, chain HD [auth J] MOL2 format, chain IA [auth B] MOL2 format, chain MB [auth F] MOL2 format, chain MD [auth K] MOL2 format, chain NC [auth I] MOL2 format, chain OC [auth I] MOL2 format, chain QD [auth L] MOL2 format, chain X [auth A] MOL2 format, chain XB [auth G] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth D] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth D] mmCIF format, chain DC [auth G] mmCIF format, chain EB [auth D] mmCIF format, chain FD [auth J] mmCIF format, chain GD [auth J] mmCIF format, chain HD [auth J] mmCIF format, chain IA [auth B] mmCIF format, chain MB [auth F] mmCIF format, chain MD [auth K] mmCIF format, chain NC [auth I] mmCIF format, chain OC [auth I] mmCIF format, chain QD [auth L] mmCIF format, chain X [auth A] mmCIF format, chain XB [auth G]	CA [auth A] CB [auth D] DA [auth A] DB [auth D] DC [auth G] CA [auth A], CB [auth D], DA [auth A], DB [auth D], DC [auth G], EB [auth D], FD [auth J], GD [auth J], HD [auth J], IA [auth B], MB [auth F], MD [auth K], NC [auth I], OC [auth I], QD [auth L], X [auth A], XB [auth G]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain CB [auth D] Focus chain DA [auth A] Focus chain DB [auth D] Focus chain DC [auth G] Focus chain EB [auth D] Focus chain FD [auth J] Focus chain GD [auth J] Focus chain HD [auth J] Focus chain IA [auth B] Focus chain MB [auth F] Focus chain MD [auth K] Focus chain NC [auth I] Focus chain OC [auth I] Focus chain QD [auth L] Focus chain X [auth A] Focus chain XB [auth G] Interactions & Density Focus chain CA [auth A] Focus chain CB [auth D] Focus chain DA [auth A] Focus chain DB [auth D] Focus chain DC [auth G] Focus chain EB [auth D] Focus chain FD [auth J] Focus chain GD [auth J] Focus chain HD [auth J] Focus chain IA [auth B] Focus chain MB [auth F] Focus chain MD [auth K] Focus chain NC [auth I] Focus chain OC [auth I] Focus chain QD [auth L] Focus chain X [auth A] Focus chain XB [auth G]
K Query on K Download Ideal Coordinates CCD File SDF format, chain NB [auth G] SDF format, chain OA [auth D] MOL2 format, chain NB [auth G] MOL2 format, chain OA [auth D] mmCIF format, chain NB [auth G] mmCIF format, chain OA [auth D]	NB [auth G], OA [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain NB [auth G] Focus chain OA [auth D] Interactions & Density Focus chain NB [auth G] Focus chain OA [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain HB [auth E] SDF format, chain HC [auth H] SDF format, chain LA [auth C] SDF format, chain LB [auth F] SDF format, chain MC [auth I] SDF format, chain OD [auth L] SDF format, chain PD [auth L] SDF format, chain Y [auth A] SDF format, chain YB [auth G] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth E] MOL2 format, chain HC [auth H] MOL2 format, chain LA [auth C] MOL2 format, chain LB [auth F] MOL2 format, chain MC [auth I] MOL2 format, chain OD [auth L] MOL2 format, chain PD [auth L] MOL2 format, chain Y [auth A] MOL2 format, chain YB [auth G] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth E] mmCIF format, chain HC [auth H] mmCIF format, chain LA [auth C] mmCIF format, chain LB [auth F] mmCIF format, chain MC [auth I] mmCIF format, chain OD [auth L] mmCIF format, chain PD [auth L] mmCIF format, chain Y [auth A] mmCIF format, chain YB [auth G]	HA [auth B] HB [auth E] HC [auth H] LA [auth C] LB [auth F] HA [auth B], HB [auth E], HC [auth H], LA [auth C], LB [auth F], MC [auth I], OD [auth L], PD [auth L], Y [auth A], YB [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain HA [auth B] Focus chain HB [auth E] Focus chain HC [auth H] Focus chain LA [auth C] Focus chain LB [auth F] Focus chain MC [auth I] Focus chain OD [auth L] Focus chain PD [auth L] Focus chain Y [auth A] Focus chain YB [auth G] Interactions & Density Focus chain HA [auth B] Focus chain HB [auth E] Focus chain HC [auth H] Focus chain LA [auth C] Focus chain LB [auth F] Focus chain MC [auth I] Focus chain OD [auth L] Focus chain PD [auth L] Focus chain Y [auth A] Focus chain YB [auth G]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain JD [auth K] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain VA [auth D] SDF format, chain VB [auth G] SDF format, chain WC [auth J] MOL2 format, chain JD [auth K] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth D] MOL2 format, chain VB [auth G] MOL2 format, chain WC [auth J] mmCIF format, chain JD [auth K] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth D] mmCIF format, chain VB [auth G] mmCIF format, chain WC [auth J]	JD [auth K] U [auth A] V [auth A] VA [auth D] VB [auth G] JD [auth K], U [auth A], V [auth A], VA [auth D], VB [auth G], WC [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain JD [auth K] Focus chain U [auth A] Focus chain V [auth A] Focus chain VA [auth D] Focus chain VB [auth G] Focus chain WC [auth J] Interactions & Density Focus chain JD [auth K] Focus chain U [auth A] Focus chain V [auth A] Focus chain VA [auth D] Focus chain VB [auth G] Focus chain WC [auth J]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain KA [auth C] SDF format, chain KD [auth K] MOL2 format, chain KA [auth C] MOL2 format, chain KD [auth K] mmCIF format, chain KA [auth C] mmCIF format, chain KD [auth K]	KA [auth C], KD [auth K]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain KA [auth C] Focus chain KD [auth K] Interactions & Density Focus chain KA [auth C] Focus chain KD [auth K]

Modified Residues 7 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AGM Query on AGM	A, D, G, J	L-PEPTIDE LINKING	C₇ H₁₇ N₄ O₂		ARG
DYA Query on DYA	A, D, G, J	L-PEPTIDE LINKING	C₄ H₅ N O₄		ASP
GL3 Query on GL3	A, D, G, J	L-PEPTIDE LINKING	C₂ H₅ N O S		GLY
MGN Query on MGN	A, D, G, J	L-PEPTIDE LINKING	C₆ H₁₂ N₂ O₃		GLN
MHS Query on MHS	A, D, G, J	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS
SMC Query on SMC	A, D, G, J	L-PEPTIDE LINKING	C₄ H₉ N O₂ S		CYS
TRX Query on TRX	A, D, G, J	L-PEPTIDE LINKING	C₁₁ H₁₂ N₂ O₃		TRP

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.155 (Depositor), 0.154 (DCC)
R-Value Work: 0.129 (Depositor), 0.128 (DCC)
R-Value Observed: 0.131 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.478	α = 90
b = 153.673	β = 90
c = 212.885	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Mueller, M.-C.

Wagner, T.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101125699
German Research Foundation (DFG)	Germany	WA 4053/1-1
Netherlands Organisation for Scientific Research (NWO)	Netherlands	VI.Vidi.223.012
Netherlands Organisation for Scientific Research (NWO)	Netherlands	024.002.002
Max Planck Society	Germany	--