1T5A

Human Pyruvate Kinase M2

Structural Biology Knowledgebase: 1T5A SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.231

Literature

Macromolecules
Sequence Display for 1T5A

Classification: TRANSFERASE

Total Structure Weight: 252703.36

Macromolecule Entities
Molecule Chains Length Organism Details
Pyruvate kinase, M2 isozyme A, B, C, D 567 Homo sapiens EC#: 2.7.1.40 IUBMB
Gene Name(s): PKM Gene View OIP3 PK2 PK3 PKM2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FBP
Query on FBP

A, B, C, D BETA-FRUCTOSE-1,6-DIPHOSPHATE
FRUCTOSE-1,6-BISPHOSPHATE (Synonym)
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B, C, D PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B, C, D GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OXL
Query on OXL

A, B, C, D OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A, B, C, D POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
OXL N/A in BindingDB
N/A in BindingMoad
Ki: 24000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.231
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 108.21 α = 90.00
b = 145.01 β = 90.00
c = 159.26 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-05-03
  • Released Date: 2005-07-12
  • Deposition author(s): Dombrauckas, J.D., Santarsiero, B.D., Mesecar, A.D.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4