SMTL ID : 5ao3.1

Crystal structure of human SAMHD1 (amino acid residues 115-626) bound to GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

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

FE.1: 6 residues within 4Å: Chain A: R.76, H.79, H.118, D.119, D.223 Ligands: SO4.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.79, A:H.118, A:D.119, A:D.223, A:D.223 FE.6: 5 residues within 4Å: Chain B: H.79, H.118, D.119, D.223 Ligands: SO4.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.79, B:H.118, B:D.119, B:D.223 FE.11: 6 residues within 4Å: Chain C: R.76, H.79, H.118, D.119, D.223 Ligands: SO4.14 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.79, C:H.118, C:D.119, C:D.223 FE.15: 6 residues within 4Å: Chain D: R.76, H.79, H.118, D.119, D.223 Ligands: SO4.19 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.79, D:H.118, D:D.119, D:D.223

4 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.2: 14 residues within 4Å: Chain A: K.28, V.29, I.30, V.45, I.48, D.49, Q.54, R.57, F.77 Chain C: Y.67, V.68, V.290, R.363, L.365 12 PLIP interactions: 3 interactions with chain C, 9 interactions with chain A Hydrogen bonds: C:R.363, A:K.28, A:K.28, A:V.29, A:Q.54, A:R.57 Salt bridges: C:R.363, A:K.28, A:K.28, A:K.28, A:D.49 pi-Cation interactions: C:R.363 GTP.12: 13 residues within 4Å: Chain A: Y.67, V.68, V.290, R.363, L.365 Chain C: K.28, V.29, I.30, V.45, D.49, Q.54, R.57, F.77 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:K.28, C:Q.54, C:R.57, A:R.363 Salt bridges: C:K.28, C:K.28, C:K.28, C:D.49, A:R.363 pi-Cation interactions: A:R.363 GTP.16: 13 residues within 4Å: Chain B: K.28, V.29, I.30, D.49, Q.54, R.57, F.77 Chain D: Y.67, V.68, V.290, R.363, L.365, K.367 11 PLIP interactions: 3 interactions with chain D, 8 interactions with chain B Salt bridges: D:R.363, D:K.367, B:K.28, B:K.28, B:K.28, B:D.49 pi-Cation interactions: D:R.363 Hydrogen bonds: B:K.28, B:V.29, B:Q.54, B:R.57 GTP.17: 14 residues within 4Å: Chain B: Y.67, V.68, V.290, R.363, L.365 Chain D: K.28, V.29, I.30, V.45, I.48, D.49, Q.54, R.57, F.77 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:K.28, D:K.28, D:V.29, D:Q.54, D:R.57 Salt bridges: D:K.28, D:K.28, D:K.28, D:D.49, B:R.363 pi-Cation interactions: B:R.363

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: G.236, I.237, Q.238, R.284 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.236, A:Q.238 Salt bridges: A:R.284 SO4.4: 6 residues within 4Å: Chain A: H.276, S.280, R.283, R.284 Chain B: R.264 Ligands: SO4.3 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.280, B:R.264 Salt bridges: A:H.276, A:R.283, A:R.284 SO4.5: 9 residues within 4Å: Chain A: R.76, H.79, H.118, D.119, H.122, H.127, H.145, D.223 Ligands: FE.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.119 Salt bridges: A:R.76, A:H.118, A:H.122, A:H.127, A:H.145 SO4.7: 6 residues within 4Å: Chain A: R.264 Chain B: H.276, S.280, R.283, R.284 Ligands: SO4.8 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.276, B:R.283, B:R.284, A:R.264 SO4.8: 5 residues within 4Å: Chain B: G.236, I.237, Q.238, R.284 Ligands: SO4.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.238 Salt bridges: B:R.284 SO4.9: 4 residues within 4Å: Chain B: G.131, R.382, Y.385, N.416 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.385, B:N.416, B:N.416 Salt bridges: B:R.382 SO4.10: 9 residues within 4Å: Chain B: R.76, H.79, H.118, D.119, H.122, H.127, H.145, D.223 Ligands: FE.6 5 PLIP interactions: 5 interactions with chain B Salt bridges: B:R.76, B:H.118, B:H.122, B:H.127, B:H.145 SO4.13: 4 residues within 4Å: Chain C: H.127, G.131, R.382, N.416 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.416, C:N.416 Salt bridges: C:R.382 SO4.14: 9 residues within 4Å: Chain C: R.76, H.79, H.118, D.119, H.122, H.127, H.145, D.223 Ligands: FE.11 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.145 Salt bridges: C:R.76, C:H.127, C:K.224 SO4.18: 3 residues within 4Å: Chain D: G.131, R.382, N.416 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.131, D:N.416, D:N.416 Salt bridges: D:R.382 SO4.19: 10 residues within 4Å: Chain D: R.76, H.79, H.118, D.119, H.122, H.127, H.145, D.223, Y.227 Ligands: FE.15 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.223 Salt bridges: D:R.76, D:H.79, D:H.118, D:H.122, D:H.127, D:H.145

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

2016-04-20

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

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