SMTL ID : 5ao2.1

Crystal structure of human SAMHD1 (amino acid residues 115-583) R164A variant bound to dGTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.97 Å

Oligo State

homo-tetramer

Ligands

4 x FE: FE (III) ION(Non-covalent)

FE.1: 4 residues within 4Å: Chain A: H.75, H.114, D.115, D.219 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.75, A:H.114, A:D.115, A:D.219, H2O.1 FE.3: 4 residues within 4Å: Chain B: H.75, H.114, D.115, D.219 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.75, B:H.114, B:D.115, B:D.219, H2O.1 FE.5: 4 residues within 4Å: Chain C: H.75, H.114, D.115, D.219 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.75, C:H.114, C:D.115, C:D.219, C:D.219 FE.8: 4 residues within 4Å: Chain D: H.75, H.114, D.115, D.219 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.75, D:H.114, D:D.115, D:D.219, D:D.219

4 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.2: 13 residues within 4Å: Chain A: Y.63, V.64, V.286, R.359, L.361 Chain B: K.24, V.25, I.26, I.44, D.45, Q.50, R.53, F.73 12 PLIP interactions: 3 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:R.359, B:K.24, B:K.24, B:Q.50, B:R.53 Salt bridges: A:R.359, B:K.24, B:K.24, B:K.24, B:D.45 pi-Cation interactions: A:R.359 Hydrophobic interactions: B:I.26 DGT.4: 13 residues within 4Å: Chain A: K.24, V.25, I.26, I.44, D.45, Q.50, R.53, F.73 Chain B: Y.63, V.64, V.286, R.359, L.361 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.26 Hydrogen bonds: A:K.24, A:K.24, A:Q.50, A:R.53, B:R.359 Salt bridges: A:K.24, A:K.24, A:K.24, A:D.45, B:R.359 pi-Cation interactions: B:R.359 DGT.6: 14 residues within 4Å: Chain C: K.24, V.25, I.26, V.41, I.44, D.45, Q.50, R.53, F.73 Chain D: Y.63, V.64, V.286, R.359, L.361 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.26 Hydrogen bonds: C:K.24, C:K.24, C:Q.50, C:R.53, D:R.359 Salt bridges: C:K.24, C:K.24, C:K.24, C:D.45, D:R.359 pi-Cation interactions: D:R.359 DGT.7: 13 residues within 4Å: Chain C: Y.63, V.64, V.286, R.359, L.361 Chain D: K.24, V.25, I.26, I.44, D.45, Q.50, R.53, F.73 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:I.26 Hydrogen bonds: D:K.24, D:K.24, D:Q.50, D:R.53, C:R.359 Salt bridges: D:K.24, D:K.24, D:K.24, D:D.45, C:R.359 pi-Cation interactions: C:R.359

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arnold, L.H. et al., Phospho-Dependent Regulation of Samhd1 Oligomerisation Couples Catalysis and Restriction. Plos Pathog. (2015)

Release Date

2015-10-14

Peptides

DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1