SMTL ID : 5ao0.1

Crystal structure of human SAMHD1 (amino acid residues 41-583) bound to ddGTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.73 Å

Oligo State

homo-tetramer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: H.149, H.188, D.189, D.293 Ligands: DG3.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.149, A:H.188, A:D.189, A:D.293 FE.5: 6 residues within 4Å: Chain B: R.146, H.149, H.188, D.189, D.293 Ligands: DG3.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.149, B:H.188, B:D.189, B:D.293 FE.9: 5 residues within 4Å: Chain C: H.149, H.188, D.189, D.293 Ligands: DG3.10 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.149, C:H.188, C:D.189, C:D.293 FE.13: 6 residues within 4Å: Chain D: R.146, H.149, H.188, D.189, D.293 Ligands: DG3.14 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.149, D:H.188, D:D.189, D:D.293

8 x DG3: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DG3.2: 15 residues within 4Å: Chain A: R.146, H.149, H.188, D.189, H.192, H.197, H.215, E.216, D.293, K.294, Y.297, H.352, Y.356, N.362 Ligands: FE.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.216, A:Y.297, A:Y.356, A:N.362 Salt bridges: A:R.146, A:H.188, A:H.192, A:H.192, A:H.197, A:H.197, A:H.215, A:K.294 DG3.3: 14 residues within 4Å: Chain A: K.98, V.99, I.100, I.118, D.119, Q.124, R.127, F.147 Chain B: Y.137, V.138, V.360, R.433, L.435 Ligands: MG.4 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.100 Hydrogen bonds: A:Q.124, A:R.127, B:R.433 Salt bridges: A:K.98, A:K.98, A:K.98, A:D.119, B:R.433 pi-Cation interactions: B:R.433 DG3.6: 17 residues within 4Å: Chain B: R.146, H.149, H.188, D.189, H.192, H.197, G.201, H.215, E.216, D.293, K.294, Y.297, H.352, Y.356, N.362, D.365 Ligands: FE.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.356 Hydrogen bonds: B:E.216, B:E.216, B:Y.297, B:Y.356, B:D.365 Salt bridges: B:R.146, B:H.188, B:H.192, B:H.192, B:H.197, B:H.197, B:H.215 pi-Stacking: B:H.197 DG3.7: 14 residues within 4Å: Chain A: Y.137, V.138, V.360, R.433, L.435 Chain B: K.98, V.99, I.100, I.118, D.119, Q.124, R.127, F.147 Ligands: MG.8 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:R.433, B:K.98, B:K.98, B:Q.124, B:R.127 Salt bridges: A:R.433, B:K.98, B:K.98, B:K.98, B:D.119 pi-Cation interactions: A:R.433 Hydrophobic interactions: B:K.98, B:I.100 DG3.10: 15 residues within 4Å: Chain C: R.146, H.149, H.188, D.189, H.192, H.197, H.215, E.216, D.293, K.294, Y.297, H.352, Y.356, N.362 Ligands: FE.9 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Y.356, C:N.362 Salt bridges: C:R.146, C:H.188, C:H.192, C:H.192, C:H.197, C:H.197, C:H.215, C:K.294 DG3.11: 14 residues within 4Å: Chain C: K.98, V.99, I.100, I.118, D.119, Q.124, R.127, F.147 Chain D: Y.137, V.138, V.360, R.433, L.435 Ligands: MG.12 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.100 Hydrogen bonds: C:Q.124, C:R.127, D:R.433 Salt bridges: C:K.98, C:K.98, C:K.98, C:D.119, D:R.433 pi-Cation interactions: D:R.433 DG3.14: 17 residues within 4Å: Chain D: R.146, H.149, H.188, D.189, H.192, H.197, G.201, H.215, E.216, D.293, K.294, Y.297, H.352, Y.356, N.362, D.365 Ligands: FE.13 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.356 Hydrogen bonds: D:H.197, D:E.216, D:Y.356 Salt bridges: D:R.146, D:H.188, D:H.192, D:H.192, D:H.197, D:H.197, D:H.215 pi-Stacking: D:H.197 DG3.15: 14 residues within 4Å: Chain C: Y.137, V.138, V.360, R.433, L.435 Chain D: K.98, V.99, I.100, I.118, D.119, Q.124, R.127, F.147 Ligands: MG.16 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:K.98, D:I.100 Hydrogen bonds: D:K.98, D:K.98, D:Q.124, D:R.127, C:R.433 Salt bridges: D:K.98, D:K.98, D:K.98, D:D.119, C:R.433 pi-Cation interactions: C:R.433

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.4: 1 residues within 4Å: Ligands: DG3.3 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: DG3.7 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: DG3.11 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Ligands: DG3.15 No protein-ligand interaction detected (PLIP)

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
A

D
B

DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1