4BZC

Crystal structure of the tetrameric dGTP-bound wild type SAMHD1 catalytic core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.190

Literature

Macromolecules
Sequence Display for 4BZC

Classification: HYDROLASE

Total Structure Weight: 260229.22

Macromolecule Entities
Molecule Chains Length Organism Details
DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1 A, B, C, D 550 Homo sapiens EC#: 3.1.5 IUBMB
Fragment: HD DOMAIN, RESIDUES 113-626
Gene Name(s): SAMHD1 Gene View MOP5
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
T8T
Query on T8T

A, B, C, D 2'-deoxyguanosine-5'-O-(1-thiotriphosphate)
C10 H16 N5 O12 P3 S
IOCRYHATDKHWPM-KUFCIHQDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, B, C, D MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.190
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 79.00 α = 90.00
b = 138.73 β = 113.56
c = 93.71 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-07-25
  • Released Date: 2013-10-23
  • Deposition author(s): Ji, X., Yang, H., Wu, Y., Yan, J., Mehrens, J., DeLucia, M., Hao, C., Gronenborn, A.M., Skowronski, J., Ahn, J., Xiong, Y.

Revision History

  • Version 1_0: 2013-10-23

    Type: Initial release

  • Version 1_1: 2013-10-30

    Type: Database references

  • Version 1_2: 2013-11-20

    Type: Database references