3ME3

Activator-Bound Structure of Human Pyruvate Kinase M2

Structural Biology Knowledgebase: 3ME3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.219

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3ME3

Classification: TRANSFERASE

Total Structure Weight: 242854.28

Macromolecule Entities
Molecule Chains Length Organism Details
Pyruvate kinase isozymes M1/M2 A, B, C, D 550 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 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
3SZ
Query on 3SZ

A, D 3-{[4-(2,3-dihydro-1,4-benzodioxin-6-ylsulfonyl)- 1,4-diazepan-1-yl]sulfonyl}aniline
C19 H23 N3 O6 S2
GMHIOMMKSMSRLY-UHFFFAOYSA-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)
SO4
Query on SO4

A, B, C, D SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNX
Query on UNX

A, B, C, D UNKNOWN ATOM OR ION
X
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
3SZ EC50: 38 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.219
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 80.88 α = 90.00
b = 152.56 β = 103.17
c = 93.04 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-03-31
  • Released Date: 2010-04-28
  • Deposition author(s): Hong, B., Dimov, S., Tempel, W., Auld, D., Thomas, C., Boxer, M., Jianq, J.-K., Skoumbourdis, A., Min, S., Southall, N., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Inglese, J., Park, H., Structural Genomics Consortium (SGC)

Revision History

  • 2013-01-02
    Type: Citation | Details: Citation update
  • 2012-11-07
    Type: Citation | Details: Citation update
  • 2012-09-12
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4