1ZNQ | pdb_00001znq

Crystal Structure of Human Liver GAPDH

• PDB DOI: https://doi.org/10.2210/pdb1ZNQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-05-11 Released: 2005-05-24 
• Deposition Author(s): Ismail, S.A., Park, H.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 

Starting Model: experimental

Literature

Crystal Structure Analysis of Human liver GAPDH

Ismail, S.A., Park, H.W.

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 (software)

Macromolecule Content 

• Total Structure Weight: 148.18 kDa 
• Atom Count: 10,418 
• Modeled Residue Count: 1,332 
• Deposited Residue Count: 1,352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase, liver	A [auth O], B [auth P], C [auth R], D [auth Q]	338	Homo sapiens	Mutation(s): 0  Gene Names: GAPD EC: 1.2.1.12 (PDB Primary Data), 2.6.99 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P04406 (Homo sapiens) Explore P04406  Go to UniProtKB:  P04406
PHAROS:  P04406 GTEx:  ENSG00000111640

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth O], F [auth P], G [auth R], H [auth Q]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.5	α = 90
b = 132.31	β = 90
c = 86.037	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-24 
Deposition Author(s): Ismail, S.A., Park, H.W.

Revision History  

• Version 1.0: 2005-05-24
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-11-12
  Changes: Structure summary
• Version 1.4: 2019-01-16
  Changes: Data collection, Structure summary
• Version 1.5: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description