2G76 | pdb_00002g76

Crystal structure of human 3-phosphoglycerate dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb2G76/pdb

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


• Deposited: 2006-02-27 Released: 2006-03-21 
• Deposition Author(s): Turnbull, A.P., Salah, E., Savitsky, P., Gileadi, O., von Delft, F., Edwards, A., Arrowsmith, C., Weigelt, J., Sundstrom, M., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of human 3-phosphoglycerate dehydrogenase

Turnbull, A.P., Salah, E., Savitsky, P., Gileadi, O., von Delft, F., Edwards, A., Arrowsmith, C., Weigelt, J., Sundstrom, M., Oppermann, U.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 73.8 kDa 
• Atom Count: 4,847 
• Modeled Residue Count: 603 
• Deposited Residue Count: 670 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-3-phosphoglycerate dehydrogenase	A, B	335	Homo sapiens	Mutation(s): 0  Gene Names: PHGDH, PGDH3 EC: 1.1.1.95 (PDB Primary Data), 1.1.1.399 (UniProt), 1.1.1.37 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O43175 (Homo sapiens) Explore O43175  Go to UniProtKB:  O43175
PHAROS:  O43175 GTEx:  ENSG00000092621

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	D [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
MLT	C [auth A], E [auth B]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.084	α = 90
b = 124.113	β = 100.99
c = 59.502	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-21 
Deposition Author(s): Turnbull, A.P., Salah, E., Savitsky, P., Gileadi, O., von Delft, F., Edwards, A., Arrowsmith, C., Weigelt, J., Sundstrom, M., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-03-21
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description