4Q7H | pdb_00004q7h

Crystal structure of SAMHD1 catalytic core with GTP

• PDB DOI: https://doi.org/10.2210/pdb4Q7H/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-04-25 Released: 2015-05-27 
• Deposition Author(s): Xiaohong, Q., Yanhong, L., Jia, K., Xiaofang, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.248 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Structural insight into activation mechanism of SAMHD1

Xiaohong, Q., Yanhong, L., Jia, K., Xiaofang, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 246.22 kDa 
• Atom Count: 14,424 
• Modeled Residue Count: 1,794 
• Deposited Residue Count: 2,104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1	A, B, C, D	526	Homo sapiens	Mutation(s): 1  Gene Names: SAMHD1, MOP5 EC: 3.1.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3Z3 (Homo sapiens) Explore Q9Y3Z3  Go to UniProtKB:  Q9Y3Z3
PHAROS:  Q9Y3Z3 GTEx:  ENSG00000101347

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	F [auth A], H [auth B], J [auth C]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN	E [auth A], G [auth B], I [auth C], K [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.248 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.943	α = 90
b = 142.765	β = 90
c = 199.501	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-27 
Deposition Author(s): Xiaohong, Q., Yanhong, L., Jia, K., Xiaofang, Y.

Revision History  

• Version 1.0: 2015-05-27
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Data collection
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary