1X0X | pdb_00001x0x

Co-Structure of Homo Sapiens Glycerol-3-Phosphate Dehydrogenase 1 complex with NAD

• PDB DOI: https://doi.org/10.2210/pdb1X0X/pdb

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


• Deposited: 2005-03-31 Released: 2006-04-11 
• Deposition Author(s): Rao, Z., Ou, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.239 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Crystal Structures of Human Glycerol 3-phosphate Dehydrogenase 1 (GPD1)

Ou, X., Ji, C., Han, X., Zhao, X., Li, X., Mao, Y., Wong, L.L., Bartlam, M., Rao, Z.

(2006) J Mol Biology 357: 858-869

• PubMed: 16460752 
• DOI: https://doi.org/10.1016/j.jmb.2005.12.074
• Primary Citation Related Structures: 
  1WPQ, 1X0V, 1X0X


• PubMed Abstract: 
  

  Homo sapiens L-alpha-glycerol-3-phosphate dehydrogenase 1 (GPD1) catalyzes the reversible biological conversion of dihydroxyacetone (DHAP) to glycerol-3-phosphate. The GPD1 protein was expressed in Escherichia coli, and purified as a fusion protein with glutathione S-transferase. Here we report the apoenzyme structure of GPD1 determined by multiwavelength anomalous diffraction phasing, and other complex structures with small molecules (NAD+ and DHAP) by the molecular replacement method. This enzyme structure is organized into two distinct domains, the N-terminal eight-stranded beta-sheet sandwich domain and the C-terminal helical substrate-binding domain. An electrophilic catalytic mechanism by the epsilon-NH3+ group of Lys204 is proposed on the basis of the structural analyses. In addition, the inhibitory effects of zinc and sulfate on GPDHs are assayed and discussed.

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, Institute of Biophysics (IBP), Chinese Academy of Sciences, Beijing 100101, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 39.16 kDa 
• Atom Count: 2,917 
• Modeled Residue Count: 350 
• Deposited Residue Count: 354 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic	A	354	Homo sapiens	Mutation(s): 0  EC: 1.1.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P21695 (Homo sapiens) Explore P21695  Go to UniProtKB:  P21695
PHAROS:  P21695 GTEx:  ENSG00000167588

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	G [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.239 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.599	α = 90
b = 116.599	β = 90
c = 153.742	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-11 
Deposition Author(s): Rao, Z., Ou, X.

Revision History  

• Version 1.0: 2006-04-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references, Derived calculations