1VC2 | pdb_00001vc2

Crystal structure of Glyceraldehyde 3-Phosphate Dehydrogenase from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb1VC2/pdb

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


• Deposited: 2004-03-04 Released: 2004-03-16 
• Deposition Author(s): Ishijima, J., Yutani, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.286 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the Glyceraldehyde 3-Phosphate Dehydrogenase from Thermus thermophilus HB8

Ishijima, J., Yutani, K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 36.61 kDa 
• Atom Count: 2,606 
• Modeled Residue Count: 331 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde 3-Phosphate Dehydrogenase	A	331	Thermus thermophilus	Mutation(s): 0  EC: 1.2.1.12 (PDB Primary Data), 1.2.1 (UniProt)
UniProt
Find proteins for P84125 (Thermus thermophilus) Explore P84125  Go to UniProtKB:  P84125

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.286 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.221	α = 90
b = 94.221	β = 90
c = 146.078	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-16 
Deposition Author(s): Ishijima, J., Yutani, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2004-03-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  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