3C3B

Crystal Structure of human phosphoglycerate kinase bound to D-CDP

Structural Biology Knowledgebase: 3C3B SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.169

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3C3B

Classification: Transferase

Total Structure Weight: 90503.72

Macromolecule Entities
Molecule Chains Length Organism Details
Phosphoglycerate kinase 1 A, B 420 Homo sapiens EC#: 2.7.2.3 IUBMB
Gene Name(s): PGK1 Gene View PGKA MIG10 OK/SW-cl.110

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

B CYTIDINE-5'-DIPHOSPHATE
C9 H15 N3 O11 P2
ZWIADYZPOWUWEW-XVFCMESISA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.169
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 35.58 α = 78.92
b = 55.59 β = 84.32
c = 93.81 γ = 82.95

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-01-28
  • Released Date: 2008-07-01
  • Deposition author(s): Arold, S.T., Gondeau, C., Lionne, C., Chaloin, L.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4