2DQ4

Crystal structure of threonine 3-dehydrogenase

PDB DOI: https://doi.org/10.2210/pdb2DQ4/pdb

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

Deposited: 2006-05-19 Released: 2007-06-12
Deposition Author(s): Omi, R., Yao, T., Goto, M., Miyahara, I., Hirotsu, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.237
R-Value Work: 0.207
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of threonine 3-dehydrogenase

Omi, R., Yao, T., Goto, M., Miyahara, I., Hirotsu, K.

To be published.

Macromolecule Content

Total Structure Weight: 74.01 kDa
Atom Count: 5,344
Modelled Residue Count: 686
Deposited Residue Count: 686
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-threonine 3-dehydrogenase	A, B	343	Thermus thermophilus	Mutation(s): 0 EC: 1.1.1.103
UniProt
Find proteins for Q5SKS4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKS4 Go to UniProtKB: Q5SKS4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SKS4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B]	E [auth A], H [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A]	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.237
R-Value Work: 0.207
R-Value Observed: 0.207
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.349	α = 90
b = 136.349	β = 90
c = 269.714	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
CrystalClear	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-06-12

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-06-12
Type: Initial release
Version 1.1: 2007-10-04
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description

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2DQ4

Crystal structure of threonine 3-dehydrogenase

Crystal structure of threonine 3-dehydrogenase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)