1PVN

The crystal structure of the complex between IMP dehydrogenase catalytic domain and a transition state analogue MZP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.196

Literature

Macromolecules
Sequence Display for 1PVN

Classification: OXIDOREDUCTASE

Total Structure Weight: 167246.02

Macromolecule Entities
Molecule Chains Length Organism Details
Inosine-5'-monophosphate dehydrogenase A, B, C, D 376 Tritrichomonas suis EC#: 1.1.1.205 IUBMB
Fragment: Catalytic core domain
Gene Name(s): IMPDH
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D 4-CARBAMOYL-1-BETA-D-RIBOFURANOSYL-IMIDAZOLIUM- 5-OLATE-5'-PHOSPHATE
C9 H12 N3 O9 P
KTKAFSMJDTUUAN-UUOKFMHZSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TRS
Query on TRS

A, B, C, D 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MZP N/A in BindingDB
Ki: 0.15 nM  BindingMOAD
Ki: 0.15 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.196
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 96.75 α = 90.00
b = 112.57 β = 90.00
c = 159.76 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-06-27
  • Released Date: 2003-07-22
  • Deposition author(s): Gan, L., Seyedsayamdost, M., Shuto, S., Matsuda, A., Petsko, G.A., Hedstrom, L.
  • This entry supercedes: 1MWF

Revision History

  • Version 1_0: 2003-07-22

    Type: Initial release

  • Version 1_1: 2008-04-29

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance

  • Version 1_3: 2017-08-02

    Type: Source and taxonomy