3PGK

The structure of yeast phosphoglycerate kinase at 0.25 nm resolution

Structural Biology Knowledgebase: 3PGK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work:

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3PGK

Classification: TRANSFERASE

Total Structure Weight: 45370.15

Macromolecule Entities
Molecule Chains Length Organism Details
PHOSPHOGLYCERATE KINASE A 416 Saccharomyces cerevisiae EC#: 2.7.2.3 IUBMB
Mutation: A261P, ΔV263, P264A, D292S, K329T, T330V, V332L
Gene Name(s): PGK1 Gene View YCR012W YCR12W

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

A ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
3PG
Query on 3PG

A 3-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
OSJPPGNTCRNQQC-UWTATZPHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
3PG Kd: 110000 nM (97) BindingDB

N/A in BindingMoad
N/A in PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
ACE
Query on ACE
A NON-POLYMER C2 H4 O --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Observed:
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 126.60 α = 90.00
b = 54.40 β = 134.40
c = 93.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1982-07-15
  • Released Date: 1982-09-24
  • Deposition author(s): Shaw, P.J., Walker, N.P., Watson, H.C.
  • Previous versions: 1PGK

Revision History

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