8YEC | pdb_00008yec

Crystal structure of L-ribulose 3-epimerase in complex with D-allulose

PDB DOI: https://doi.org/10.2210/pdb8YEC/pdb

Classification: ISOMERASE
Organism(s): Arthrobacter globiformis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-02-22 Released: 2025-02-12
Deposition Author(s): Watanabe, M., Nakamichi, Y., Mine, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.255 (Depositor), 0.257 (DCC)
R-Value Work:
0.207 (Depositor), 0.209 (DCC)
R-Value Observed:
0.210 (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

Crystal structure of L-ribulose 3-epimerase in complex with D-allulose

Watanabe, M., Nakamichi, Y., Mine, S.

To be published.

Macromolecule Content

Total Structure Weight: 523.62 kDa
Atom Count: 36,802
Modelled Residue Count: 4,678
Deposited Residue Count: 4,752
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketose 3-epimerase	A [auth E] B [auth F] C [auth A] D [auth B] E [auth C] A [auth E], B [auth F], C [auth A], D [auth B], E [auth C], F [auth D], G, H, I, J, K, L, M, N, O, P	297	Arthrobacter globiformis	Mutation(s): 0 Gene Names: DAE EC: 5.1.3
UniProt
Find proteins for A0A1L7NQ96 (Arthrobacter globiformis) Explore A0A1L7NQ96 Go to UniProtKB: A0A1L7NQ96
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1L7NQ96
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FUD (Subject of Investigation/LOI) Query on FUD Download Ideal Coordinates CCD File SDF format, chain BB [auth K] SDF format, chain CA [auth B] SDF format, chain FA [auth C] SDF format, chain FB [auth L] SDF format, chain IB [auth M] SDF format, chain KA [auth D] SDF format, chain MB [auth N] SDF format, chain NA [auth G] SDF format, chain PB [auth O] SDF format, chain R [auth E] SDF format, chain RA [auth H] SDF format, chain TB [auth P] SDF format, chain UA [auth I] SDF format, chain V [auth F] SDF format, chain Y [auth A] SDF format, chain YA [auth J] MOL2 format, chain BB [auth K] MOL2 format, chain CA [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth L] MOL2 format, chain IB [auth M] MOL2 format, chain KA [auth D] MOL2 format, chain MB [auth N] MOL2 format, chain NA [auth G] MOL2 format, chain PB [auth O] MOL2 format, chain R [auth E] MOL2 format, chain RA [auth H] MOL2 format, chain TB [auth P] MOL2 format, chain UA [auth I] MOL2 format, chain V [auth F] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth J] mmCIF format, chain BB [auth K] mmCIF format, chain CA [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain FB [auth L] mmCIF format, chain IB [auth M] mmCIF format, chain KA [auth D] mmCIF format, chain MB [auth N] mmCIF format, chain NA [auth G] mmCIF format, chain PB [auth O] mmCIF format, chain R [auth E] mmCIF format, chain RA [auth H] mmCIF format, chain TB [auth P] mmCIF format, chain UA [auth I] mmCIF format, chain V [auth F] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth J]	BB [auth K] CA [auth B] FA [auth C] FB [auth L] IB [auth M] BB [auth K], CA [auth B], FA [auth C], FB [auth L], IB [auth M], KA [auth D], MB [auth N], NA [auth G], PB [auth O], R [auth E], RA [auth H], TB [auth P], UA [auth I], V [auth F], Y [auth A], YA [auth J]	D-fructose C₆ H₁₂ O₆ BJHIKXHVCXFQLS-UYFOZJQFSA-N		Interactions Focus chain BB [auth K] Focus chain CA [auth B] Focus chain FA [auth C] Focus chain FB [auth L] Focus chain IB [auth M] Focus chain KA [auth D] Focus chain MB [auth N] Focus chain NA [auth G] Focus chain PB [auth O] Focus chain R [auth E] Focus chain RA [auth H] Focus chain TB [auth P] Focus chain UA [auth I] Focus chain V [auth F] Focus chain Y [auth A] Focus chain YA [auth J] Interactions & Density Focus chain BB [auth K] Focus chain CA [auth B] Focus chain FA [auth C] Focus chain FB [auth L] Focus chain IB [auth M] Focus chain KA [auth D] Focus chain MB [auth N] Focus chain NA [auth G] Focus chain PB [auth O] Focus chain R [auth E] Focus chain RA [auth H] Focus chain TB [auth P] Focus chain UA [auth I] Focus chain V [auth F] Focus chain Y [auth A] Focus chain YA [auth J]
PSJ (Subject of Investigation/LOI) Query on PSJ Download Ideal Coordinates CCD File SDF format, chain AB [auth K] SDF format, chain BA [auth B] SDF format, chain EA [auth C] SDF format, chain EB [auth L] SDF format, chain HB [auth M] SDF format, chain JA [auth D] SDF format, chain LB [auth N] SDF format, chain MA [auth G] SDF format, chain OB [auth O] SDF format, chain Q [auth E] SDF format, chain QA [auth H] SDF format, chain SB [auth P] SDF format, chain TA [auth I] SDF format, chain U [auth F] SDF format, chain X [auth A] SDF format, chain XA [auth J] MOL2 format, chain AB [auth K] MOL2 format, chain BA [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth L] MOL2 format, chain HB [auth M] MOL2 format, chain JA [auth D] MOL2 format, chain LB [auth N] MOL2 format, chain MA [auth G] MOL2 format, chain OB [auth O] MOL2 format, chain Q [auth E] MOL2 format, chain QA [auth H] MOL2 format, chain SB [auth P] MOL2 format, chain TA [auth I] MOL2 format, chain U [auth F] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth J] mmCIF format, chain AB [auth K] mmCIF format, chain BA [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain EB [auth L] mmCIF format, chain HB [auth M] mmCIF format, chain JA [auth D] mmCIF format, chain LB [auth N] mmCIF format, chain MA [auth G] mmCIF format, chain OB [auth O] mmCIF format, chain Q [auth E] mmCIF format, chain QA [auth H] mmCIF format, chain SB [auth P] mmCIF format, chain TA [auth I] mmCIF format, chain U [auth F] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth J]	AB [auth K] BA [auth B] EA [auth C] EB [auth L] HB [auth M] AB [auth K], BA [auth B], EA [auth C], EB [auth L], HB [auth M], JA [auth D], LB [auth N], MA [auth G], OB [auth O], Q [auth E], QA [auth H], SB [auth P], TA [auth I], U [auth F], X [auth A], XA [auth J]	D-psicose C₆ H₁₂ O₆ BJHIKXHVCXFQLS-PUFIMZNGSA-N		Interactions Focus chain AB [auth K] Focus chain BA [auth B] Focus chain EA [auth C] Focus chain EB [auth L] Focus chain HB [auth M] Focus chain JA [auth D] Focus chain LB [auth N] Focus chain MA [auth G] Focus chain OB [auth O] Focus chain Q [auth E] Focus chain QA [auth H] Focus chain SB [auth P] Focus chain TA [auth I] Focus chain U [auth F] Focus chain X [auth A] Focus chain XA [auth J] Interactions & Density Focus chain AB [auth K] Focus chain BA [auth B] Focus chain EA [auth C] Focus chain EB [auth L] Focus chain HB [auth M] Focus chain JA [auth D] Focus chain LB [auth N] Focus chain MA [auth G] Focus chain OB [auth O] Focus chain Q [auth E] Focus chain QA [auth H] Focus chain SB [auth P] Focus chain TA [auth I] Focus chain U [auth F] Focus chain X [auth A] Focus chain XA [auth J]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain IA [auth C] MOL2 format, chain IA [auth C] mmCIF format, chain IA [auth C]	IA [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Interactions & Density Focus chain IA [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain CB [auth K] SDF format, chain DA [auth B] SDF format, chain GA [auth C] SDF format, chain GB [auth L] SDF format, chain JB [auth M] SDF format, chain LA [auth D] SDF format, chain NB [auth N] SDF format, chain OA [auth G] SDF format, chain QB [auth O] SDF format, chain S [auth E] SDF format, chain SA [auth H] SDF format, chain UB [auth P] SDF format, chain VA [auth I] SDF format, chain W [auth F] SDF format, chain Z [auth A] SDF format, chain ZA [auth J] MOL2 format, chain CB [auth K] MOL2 format, chain DA [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth L] MOL2 format, chain JB [auth M] MOL2 format, chain LA [auth D] MOL2 format, chain NB [auth N] MOL2 format, chain OA [auth G] MOL2 format, chain QB [auth O] MOL2 format, chain S [auth E] MOL2 format, chain SA [auth H] MOL2 format, chain UB [auth P] MOL2 format, chain VA [auth I] MOL2 format, chain W [auth F] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth J] mmCIF format, chain CB [auth K] mmCIF format, chain DA [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain GB [auth L] mmCIF format, chain JB [auth M] mmCIF format, chain LA [auth D] mmCIF format, chain NB [auth N] mmCIF format, chain OA [auth G] mmCIF format, chain QB [auth O] mmCIF format, chain S [auth E] mmCIF format, chain SA [auth H] mmCIF format, chain UB [auth P] mmCIF format, chain VA [auth I] mmCIF format, chain W [auth F] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth J]	CB [auth K] DA [auth B] GA [auth C] GB [auth L] JB [auth M] CB [auth K], DA [auth B], GA [auth C], GB [auth L], JB [auth M], LA [auth D], NB [auth N], OA [auth G], QB [auth O], S [auth E], SA [auth H], UB [auth P], VA [auth I], W [auth F], Z [auth A], ZA [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CB [auth K] Focus chain DA [auth B] Focus chain GA [auth C] Focus chain GB [auth L] Focus chain JB [auth M] Focus chain LA [auth D] Focus chain NB [auth N] Focus chain OA [auth G] Focus chain QB [auth O] Focus chain S [auth E] Focus chain SA [auth H] Focus chain UB [auth P] Focus chain VA [auth I] Focus chain W [auth F] Focus chain Z [auth A] Focus chain ZA [auth J] Interactions & Density Focus chain CB [auth K] Focus chain DA [auth B] Focus chain GA [auth C] Focus chain GB [auth L] Focus chain JB [auth M] Focus chain LA [auth D] Focus chain NB [auth N] Focus chain OA [auth G] Focus chain QB [auth O] Focus chain S [auth E] Focus chain SA [auth H] Focus chain UB [auth P] Focus chain VA [auth I] Focus chain W [auth F] Focus chain Z [auth A] Focus chain ZA [auth J]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain DB [auth K] SDF format, chain HA [auth C] SDF format, chain KB [auth N] SDF format, chain PA [auth G] SDF format, chain RB [auth O] SDF format, chain T [auth E] SDF format, chain WA [auth J] MOL2 format, chain AA [auth A] MOL2 format, chain DB [auth K] MOL2 format, chain HA [auth C] MOL2 format, chain KB [auth N] MOL2 format, chain PA [auth G] MOL2 format, chain RB [auth O] MOL2 format, chain T [auth E] MOL2 format, chain WA [auth J] mmCIF format, chain AA [auth A] mmCIF format, chain DB [auth K] mmCIF format, chain HA [auth C] mmCIF format, chain KB [auth N] mmCIF format, chain PA [auth G] mmCIF format, chain RB [auth O] mmCIF format, chain T [auth E] mmCIF format, chain WA [auth J]	AA [auth A] DB [auth K] HA [auth C] KB [auth N] PA [auth G] AA [auth A], DB [auth K], HA [auth C], KB [auth N], PA [auth G], RB [auth O], T [auth E], WA [auth J]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain DB [auth K] Focus chain HA [auth C] Focus chain KB [auth N] Focus chain PA [auth G] Focus chain RB [auth O] Focus chain T [auth E] Focus chain WA [auth J] Interactions & Density Focus chain AA [auth A] Focus chain DB [auth K] Focus chain HA [auth C] Focus chain KB [auth N] Focus chain PA [auth G] Focus chain RB [auth O] Focus chain T [auth E] Focus chain WA [auth J]