3CJ9

Structure of Rattus norvegicus NTPDase2 in complex with calcium, AMP and phosphate

Structural Biology Knowledgebase: 3CJ9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.162

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3CJ9

Classification: HYDROLASE

Total Structure Weight: 51094.77

Macromolecule Entities
Molecule Chains Length Organism Details
Ectonucleoside triphosphate diphosphohydrolase 2 A 456 Rattus norvegicus Fragment: Ectodomain, Extracellular domain, UNP residues 29-461
Gene Name(s): Entpd2 Cd39l1

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

A ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.162
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 41.06 α = 90.00
b = 69.21 β = 90.00
c = 164.36 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-03-12
  • Released Date: 2008-04-29
  • Deposition author(s): Zebisch, M., Strater, N.

Revision History

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