3VM6

Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1 in complex with alpha-D-ribose-1,5-bisphosphate

PDB DOI: https://doi.org/10.2210/pdb3VM6/pdb

Classification: ISOMERASE
Organism(s): Thermococcus kodakarensis KOD1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-12-08 Released: 2012-04-25
Deposition Author(s): Nakamura, A., Fujihashi, M., Aono, R., Sato, T., Nishiba, Y., Yoshida, S., Yano, A., Atomi, H., Imanaka, T., Miki, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.262
R-Value Work: 0.201
R-Value Observed: 0.201

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 117.45 kDa
Atom Count: 7,930
Modelled Residue Count: 963
Deposited Residue Count: 1,014
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor eIF-2B, delta subunit	A, B, C	338	Thermococcus kodakarensis KOD1	Mutation(s): 1 Gene Names: E2b2, TK0185 EC: 5.3.1
UniProt
Find proteins for Q5JFM9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JFM9 Go to UniProtKB: Q5JFM9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JFM9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RI2 Query on RI2 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain P [auth C] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C]	D [auth A], J [auth B], P [auth C]	1,5-di-O-phosphono-alpha-D-ribofuranose C₅ H₁₂ O₁₁ P₂ AAAFZMYJJHWUPN-TXICZTDVSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain P [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain P [auth C]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B]	L [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C]	E [auth A] F [auth A] G [auth A] K [auth B] M [auth B] E [auth A], F [auth A], G [auth A], K [auth B], M [auth B], N [auth B], Q [auth C], R [auth C], S [auth C], T [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain U [auth C] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C]	H [auth A], O [auth B], U [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain O [auth B] Focus chain U [auth C] Interactions & Density Focus chain H [auth A] Focus chain O [auth B] Focus chain U [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain V [auth C] MOL2 format, chain I [auth A] MOL2 format, chain V [auth C]	I [auth A], V [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain V [auth C] Interactions & Density Focus chain I [auth A] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.262
R-Value Work: 0.201
R-Value Observed: 0.201
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.537	α = 90
b = 146.537	β = 90
c = 99.649	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-04-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-04-25
Type: Initial release
Version 1.1: 2013-06-12
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary