2YBE

THE STRUCTURE OF THE FULLY CLOSED CONFORMATION OF HUMAN PGK IN COMPLEX WITH L-ADP, 3PG AND THE TSA ALUMINIUM TETRAFLUORIDE AT 2.0 A RESOLUTION

Structural Biology Knowledgebase: 2YBE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.193

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YBE

Classification: TRANSFERASE

Total Structure Weight: 45449.02

Macromolecule Entities
Molecule Chains Length Organism Details
PHOSPHOGLYCERATE KINASE 1 A 417 Homo sapiens EC#: 2.7.2.3 IUBMB
Gene Name(s): PGK1 Gene View PGKA MIG10 OK/SW-cl.110
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
LA8
Query on LA8

A L-ADENOSINE-5'-DIPHOSPHATE
L-ADP (Synonym)
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-DEGSGYPDSA-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)
ALF
Query on ALF

A TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.193
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 39.20 α = 90.00
b = 91.03 β = 90.00
c = 108.81 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-03-07
  • Released Date: 2011-04-27
  • Deposition author(s): Bowler, M.W., Chaloin, L., Lionne, C.

Revision History

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