4BR0

rat NTPDase2 in complex with Ca AMPNP

Structural Biology Knowledgebase: 4BR0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.169

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4BR0

Classification: HYDROLASE

Total Structure Weight: 51626.35

Macromolecule Entities
Molecule Chains Length Organism Details
ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 2 A 457 Rattus norvegicus Fragment: RESIDUES 28-462
Mutation: P127L, F128L
Gene Name(s): Entpd2 Cd39l1

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AU1
Query on AU1

A 5'-O-[(R)-hydroxy(phosphonoamino)phosphoryl]adenosine
Adenosine 5-(alpha,beta-imido)diphosphate (Synonym)
C10 H16 N6 O9 P2
FJNYKURUYWTJIG-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
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: 2.05 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.169
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 41.17 α = 90.00
b = 69.13 β = 90.00
c = 164.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-06-03
  • Released Date: 2013-07-17
  • Deposition author(s): Zebisch, M., Schaefer, P., Lauble, P., Straeter, N.

Revision History

  • 2013-12-25
    Type: Function and keywords | Details: KEYWDS
  • 2013-08-28
    Type: Citation | Details: JRNL