8D94

SAMHD1-DNA complex

  • Classification: HYDROLASE/DNA
  • Organism(s): Homo sapiens, synthetic construct
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-06-09 Released: 2023-07-05 
  • Deposition Author(s): Hollis, T.J., Batalis, S.M.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

SAMHD1-DNA complex

Hollis, T.J., Batalis, S.M.

To be published.

Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
A, B, C, D
626Homo sapiensMutation(s): 0 
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3Z3
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*GP*T)-3')E [auth F],
F [auth G],
G [auth H],
H [auth I]		5synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE (Subject of Investigation/LOI)
Query on FE
Download Ideal Coordinates CCD File 
I [auth A],
K [auth B],
M [auth C],
O [auth D]		FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA
Download Ideal Coordinates CCD File 
J [auth A],
L [auth B],
N [auth C],
P [auth D]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.116α = 90
b = 179.936β = 108.95
c = 79.792γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM108827A
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32-GM095440
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesT32-AI007401
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30CA012197-47

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection
  • Version 1.2: 2024-10-23
    Changes: Structure summary