9MVA | pdb_00009mva

Mycobacterium abscessus Eis2 in complex with Non-hydrolyzable CoenzymeA

PDB DOI: https://doi.org/10.2210/pdb9MVA/pdb

Classification: ANTIBIOTIC
Organism(s): Mycobacteroides abscessus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-01-15 Released: 2025-01-29
Deposition Author(s): Jayasinghe, T.D., Coker, A.L., Rajendra, T., Miller, D., Lee, R.E.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.222 (Depositor), 0.223 (DCC)
R-Value Work:
0.191 (Depositor), 0.192 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Mycobacterium abscessus Eis2 in complex with Non-hydrolyzable CoenzymeA

Jayasinghe, T.D., Coker, A.L., Rajendra, T., Miller, D., Lee, R.E.

To be published.

Macromolecule Content

Total Structure Weight: 280.76 kDa
Atom Count: 22,281
Modelled Residue Count: 2,452
Deposited Residue Count: 2,472
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amikacin resistance N-acetyltransferase Eis2	A, B, C, D, E A, B, C, D, E, F	412	Mycobacteroides abscessus	Mutation(s): 0 Gene Names: eis_2, D2E76_13785, DDJ47_01400, ERS075604_03569
UniProt
Find proteins for A0A418L6F2 (Mycobacteroides abscessus) Explore A0A418L6F2 Go to UniProtKB: A0A418L6F2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A418L6F2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SOP (Subject of Investigation/LOI) Query on SOP Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain DB [auth F] SDF format, chain H [auth A] SDF format, chain JA [auth D] SDF format, chain P [auth B] SDF format, chain TA [auth E] MOL2 format, chain AA [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain H [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain TA [auth E] mmCIF format, chain AA [auth C] mmCIF format, chain DB [auth F] mmCIF format, chain H [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain TA [auth E]	AA [auth C] DB [auth F] H [auth A] JA [auth D] P [auth B] AA [auth C], DB [auth F], H [auth A], JA [auth D], P [auth B], TA [auth E]	[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-3-HYDROXY-2,2-DIMETHYL-4-OXO-4-{[3-OXO-3-({2-[(2-OXOPROPYL)THIO]ETHYL}AMINO)PROPYL]AMINO}BUTYL DIHYDROGEN DIPHOSPHATE C₂₄ H₄₀ N₇ O₁₇ P₃ S GAMKENBUYYJLCQ-NDZSKPAWSA-N		Interactions Focus chain AA [auth C] Focus chain DB [auth F] Focus chain H [auth A] Focus chain JA [auth D] Focus chain P [auth B] Focus chain TA [auth E] Interactions & Density Focus chain AA [auth C] Focus chain DB [auth F] Focus chain H [auth A] Focus chain JA [auth D] Focus chain P [auth B] Focus chain TA [auth E]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain EB [auth F] SDF format, chain I [auth A] SDF format, chain IB [auth F] SDF format, chain KA [auth D] SDF format, chain R [auth B] SDF format, chain VA [auth E] SDF format, chain WA [auth E] SDF format, chain YA [auth E] MOL2 format, chain CA [auth C] MOL2 format, chain EB [auth F] MOL2 format, chain I [auth A] MOL2 format, chain IB [auth F] MOL2 format, chain KA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain WA [auth E] MOL2 format, chain YA [auth E] mmCIF format, chain CA [auth C] mmCIF format, chain EB [auth F] mmCIF format, chain I [auth A] mmCIF format, chain IB [auth F] mmCIF format, chain KA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain WA [auth E] mmCIF format, chain YA [auth E]	CA [auth C] EB [auth F] I [auth A] IB [auth F] KA [auth D] CA [auth C], EB [auth F], I [auth A], IB [auth F], KA [auth D], R [auth B], VA [auth E], WA [auth E], YA [auth E]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain EB [auth F] Focus chain I [auth A] Focus chain IB [auth F] Focus chain KA [auth D] Focus chain R [auth B] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain YA [auth E] Interactions & Density Focus chain CA [auth C] Focus chain EB [auth F] Focus chain I [auth A] Focus chain IB [auth F] Focus chain KA [auth D] Focus chain R [auth B] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain YA [auth E]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FB [auth F] SDF format, chain GB [auth F] SDF format, chain HB [auth F] SDF format, chain J [auth A] SDF format, chain JB [auth F] SDF format, chain K [auth A] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain UA [auth E] SDF format, chain XA [auth E] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FB [auth F] MOL2 format, chain GB [auth F] MOL2 format, chain HB [auth F] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth F] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain XA [auth E] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FB [auth F] mmCIF format, chain GB [auth F] mmCIF format, chain HB [auth F] mmCIF format, chain J [auth A] mmCIF format, chain JB [auth F] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain XA [auth E]	DA [auth C] EA [auth C] FB [auth F] GB [auth F] HB [auth F] DA [auth C], EA [auth C], FB [auth F], GB [auth F], HB [auth F], J [auth A], JB [auth F], K [auth A], LA [auth D], MA [auth D], NA [auth D], Q [auth B], S [auth B], T [auth B], U [auth B], UA [auth E], XA [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FB [auth F] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain J [auth A] Focus chain JB [auth F] Focus chain K [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain Q [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth E] Focus chain XA [auth E] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FB [auth F] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain J [auth A] Focus chain JB [auth F] Focus chain K [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain Q [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth E] Focus chain XA [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CB [auth F] SDF format, chain G [auth A] SDF format, chain IA [auth D] SDF format, chain O [auth B] SDF format, chain SA [auth E] SDF format, chain Z [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CB [auth F] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain Z [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CB [auth F] mmCIF format, chain G [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain Z [auth C]	BA [auth C] CB [auth F] G [auth A] IA [auth D] O [auth B] BA [auth C], CB [auth F], G [auth A], IA [auth D], O [auth B], SA [auth E], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CB [auth F] Focus chain G [auth A] Focus chain IA [auth D] Focus chain O [auth B] Focus chain SA [auth E] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth C] Focus chain CB [auth F] Focus chain G [auth A] Focus chain IA [auth D] Focus chain O [auth B] Focus chain SA [auth E] Focus chain Z [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain KB [auth F] SDF format, chain L [auth A] SDF format, chain OA [auth D] SDF format, chain V [auth B] SDF format, chain ZA [auth E] MOL2 format, chain FA [auth C] MOL2 format, chain KB [auth F] MOL2 format, chain L [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain ZA [auth E] mmCIF format, chain FA [auth C] mmCIF format, chain KB [auth F] mmCIF format, chain L [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain ZA [auth E]	FA [auth C] KB [auth F] L [auth A] OA [auth D] V [auth B] FA [auth C], KB [auth F], L [auth A], OA [auth D], V [auth B], ZA [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain FA [auth C] Focus chain KB [auth F] Focus chain L [auth A] Focus chain OA [auth D] Focus chain V [auth B] Focus chain ZA [auth E] Interactions & Density Focus chain FA [auth C] Focus chain KB [auth F] Focus chain L [auth A] Focus chain OA [auth D] Focus chain V [auth B] Focus chain ZA [auth E]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain BB [auth E] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain LB [auth F] SDF format, chain M [auth A] SDF format, chain MB [auth F] SDF format, chain N [auth A] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain AB [auth E] MOL2 format, chain BB [auth E] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain LB [auth F] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth F] MOL2 format, chain N [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain AB [auth E] mmCIF format, chain BB [auth E] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain LB [auth F] mmCIF format, chain M [auth A] mmCIF format, chain MB [auth F] mmCIF format, chain N [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	AB [auth E] BB [auth E] GA [auth C] HA [auth C] LB [auth F] AB [auth E], BB [auth E], GA [auth C], HA [auth C], LB [auth F], M [auth A], MB [auth F], N [auth A], PA [auth D], QA [auth D], RA [auth D], W [auth B], X [auth B], Y [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain BB [auth E] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain LB [auth F] Focus chain M [auth A] Focus chain MB [auth F] Focus chain N [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain AB [auth E] Focus chain BB [auth E] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain LB [auth F] Focus chain M [auth A] Focus chain MB [auth F] Focus chain N [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]