2P5U

Crystal structure of Thermus thermophilus HB8 UDP-glucose 4-epimerase complex with NAD

PDB DOI: https://doi.org/10.2210/pdb2P5U/pdb

Classification: ISOMERASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-03-16 Released: 2007-04-17
Deposition Author(s): Fu, Z.-Q., Chen, L., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Zhao, M., Dillard, B., Chrzas, J., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG), RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free:
0.261 (Depositor), 0.220 (DCC)
R-Value Work:
0.235 (Depositor), 0.220 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Thermus thermophilus HB8 UDP-glucose 4-epimerase complex with NAD

Fu, Z.-Q., Chen, L., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Zhao, M., Dillard, B., Chrzas, J., Rose, J.P., Wang, B.-C.

To be published.

Macromolecule Content

Total Structure Weight: 137.92 kDa
Atom Count: 10,139
Modelled Residue Count: 1,244
Deposited Residue Count: 1,244
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose 4-epimerase	A, B, C, D	311	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: TTHA0591 EC: 5.1.3.2
UniProt
Find proteins for Q5SKQ2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKQ2 Go to UniProtKB: Q5SKQ2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SKQ2
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] MOL2 format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] mmCIF format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C]	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.261 (Depositor), 0.220 (DCC)
R-Value Work: 0.235 (Depositor), 0.220 (DCC)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 250.922	α = 90
b = 250.922	β = 90
c = 121.036	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SGXPRO	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-04-17

Deposition Author(s):

Southeast Collaboratory for Structural Genomics (SECSG)

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-04-17
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-01-24
Changes: Database references, Structure summary
Version 1.5: 2024-02-21
Changes: Data collection, Database references, Derived calculations