4FXF

Structure of M2 pyruvate kinase in complex with phenylalanine

Structural Biology Knowledgebase: 4FXF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.212

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4FXF

Classification: TRANSFERASE

Total Structure Weight: 243687.93

Macromolecule Entities
Molecule Chains Length Organism Details
Pyruvate kinase isozymes M1/M2 A, B, C, D 551 Homo sapiens EC#: 2.7.1.40 IUBMB
Mutation: H379N
Gene Name(s): PKM Gene View OIP3 PK2 PK3 PKM2

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

B, D ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
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)
OXL
Query on OXL

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

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

A, B, C, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
FBP N/A in BindingDB
N/A in BindingMoad
IC50: 6500 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.212
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 81.60 α = 90.00
b = 139.35 β = 90.52
c = 111.28 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-03
  • Released Date: 2013-03-27
  • Deposition author(s): Walkinshaw, M.D., Morgan, H.P.

Revision History

  • 2013-04-24
    Type: Citation | Details: Citation update