4B2D

human PKM2 with L-serine and FBP bound.

Structural Biology Knowledgebase: 4B2D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.174

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4B2D

Classification: TRANSFERASE

Total Structure Weight: 241159.04

Macromolecule Entities
Molecule Chains Length Organism Details
PYRUVATE KINASE ISOZYMES M1/M2 A, B, C 548 Homo sapiens EC#: 2.7.1.40 IUBMB
Gene Name(s): PKM Gene View OIP3 PK2 PK3 PKM2
PYRUVATE KINASE ISOZYMES M1/M2 D 548 Homo sapiens EC#: 2.7.1.40 IUBMB
Mutation: I142L
Gene Name(s): PKM Gene View OIP3 PK2 PK3 PKM2

Small Molecules
Ligands 3 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SER
Query on SER

A, B, C, D SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-REOHCLBHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
SER N/A in BindingDB
Kd: 200000 nM  BindingMOAD
Kd: 200000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.174
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 80.61 α = 90.00
b = 151.10 β = 102.01
c = 91.79 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-13
  • Released Date: 2012-10-10
  • Deposition author(s): Chaneton, B., Hillmann, P., Zheng, L., Martin, A.C.L., Maddocks, O.D.K., Chokkathukalam, A., Coyle, J.E., Jankevics, A., Holding, F.P., Vousden, K.H., Frezza, C., OReilly, M., Gottlieb, E.

Revision History

  • 2013-02-06
    Type: Other | Details: TER, ANISOU
  • 2013-02-06
    Type: Atom nomenclature | Details: ATOM, HETATM
  • 2013-02-06
    Type: Linkage | Details: CONECT
  • 2012-11-21
    Type: Citation | Details: JRNL
  • 2012-10-24
    Type: Citation | Details: JRNL