2G76

Crystal structure of human 3-phosphoglycerate dehydrogenase

Structural Biology Knowledgebase: 2G76 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.181

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2G76

Classification: OXIDOREDUCTASE

Total Structure Weight: 73798.37

Macromolecule Entities
Molecule Chains Length Organism Details
D-3-phosphoglycerate dehydrogenase A, B 335 Homo sapiens EC#: 1.1.1.95 IUBMB
Fragment: residues 3-314
Gene Name(s): PHGDH Gene View PGDH3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAD
Query on NAD

A, B NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MLT
Query on MLT

A, B D-MALATE
(2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY- SUCCINIC ACID (Synonym)
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.181
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 43.08 α = 90.00
b = 124.11 β = 100.99
c = 59.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-02-27
  • 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

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor