1M51

PEPCK complex with a GTP-competitive inhibitor

Structural Biology Knowledgebase: 1M51 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 1M51

Classification: LYASE

Total Structure Weight: 70163.81

Macromolecule Entities
Molecule Chains Length Organism Details
phosphoenolpyruvate carboxykinase, cytosolic A 625 Homo sapiens EC#: 4.1.1.32 IUBMB
Mutation: I267V, E586D, E597V
Gene Name(s): PCK1 Gene View PEPCK1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TSX
Query on TSX

A N-[4-(1-ALLYL-3-BUTYL-2,6-DIOXO-2,3,6,7-TETRAHYDRO- 1H-PURIN-8-YLMETHYL)-PHENYL]-ACETAMIDE
1-ALLYL-3-BUTYL-8-(N-ACETYL-4-AMINOBENZYL)- XANTHINE (Synonym)
C21 H25 N5 O3
XFOWZKUTPKXWIE-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
TSX N/A in BindingDB
IC50: 18800 nM  BindingMOAD
IC50: 18800 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.178
  • Space Group: P 1

Unit Cell:

Length (Å) Angle (°)
a = 45.41 α = 88.91
b = 61.07 β = 70.21
c = 62.01 γ = 72.62

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-07-06
  • Released Date: 2003-09-30
  • Deposition author(s): Foley, L.H., Wang, P., Dunten, P., Wertheimer, S.J.

Revision History

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