RCSB PDB - 2CZC: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Pyrococcus horikoshii OT3

 2CZC

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Pyrococcus horikoshii OT3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.205 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NADClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Pyrococcus horikoshii OT3

Ito, K.Arai, R.Kamo-Uchikubo, T.Shirouzu, M.Yokoyama, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase
A, B, C, D
334Pyrococcus horikoshii OT3Mutation(s): 0 
Gene Names: PH1830
EC: 1.2.1.59
UniProt
Find proteins for O59494 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O59494 
Go to UniProtKB:  O59494
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO59494
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
K [auth C],
M [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
H [auth B],
J [auth C],
L [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.693α = 90
b = 127.192β = 90
c = 161.454γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NADClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description