6TXE

Crystal structure of tetrameric human wt-SAMHD1 (residues 109-626) with GTP, dATP, dTMPNPP and Mg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation 3D Report Full Report



Literature

Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis

Morris, E.R.Kunzelmann, S.Caswell, S.J.Arnold, L.H.Purkiss, A.G.Kelly, G.Taylor, I.A.

(2020) Nat Commun 


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
520Homo sapiensMutation(s): 0 
Gene Names: SAMHD1MOP5
EC: 3.1.5
Find proteins for Q9Y3Z3 (Homo sapiens)
Go to UniProtKB:  Q9Y3Z3
NIH Common Fund Data Resources
PHAROS  Q9Y3Z3
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download CCD File 
A, B, D, E, F, G, H, I, K, L, M, N, O, P
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
DTP
Query on DTP

Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
1FZ
Query on 1FZ

Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine
C10 H18 N3 O13 P3
YRKUYVYMPXAOAT-XLPZGREQSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
B, C, D, E, F, H, I, J, K, N, O
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE
Query on FE

Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.482α = 90
b = 172.232β = 95.31
c = 275.271γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom108014/Z/15/Z
Wellcome TrustUnited KingdomFC001029
Medical Research Council (MRC, United Kingdom)United KingdomFC001029
Cancer Research UKUnited KingdomFC001029

Revision History 

  • Version 1.0: 2020-06-24
    Type: Initial release