SMTL ID : 7ujn.1

Structure of Human SAMHD1 with Non-Hydrolysable dGTP Analog

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

12 x T8T: 2'-deoxyguanosine-5'-O-(1-thiotriphosphate)(Non-covalent)(Covalent)

T8T.1: 13 residues within 4Å: Chain A: Q.149, L.150, R.164, D.207, H.215, D.311, K.312, Y.315, D.319, R.366, H.370, Y.374, Q.375 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.150, A:Y.374 Hydrogen bonds: A:Q.149, A:R.164, A:Y.315, A:Y.315, A:Y.315, A:D.319, A:Q.375 Salt bridges: A:K.312, A:R.366 pi-Stacking: A:H.215, A:H.215, A:Y.374 pi-Cation interactions: A:H.215 T8T.2: 15 residues within 4Å: Chain A: Y.155, V.156, V.378, R.451, K.455 Chain B: K.116, V.117, I.118, I.136, D.137, Q.142, R.145, F.165 Chain D: K.523 Ligands: T8T.6 14 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: B:I.118 Hydrogen bonds: B:Q.142, B:R.145, B:R.145, A:R.451, A:R.451 Salt bridges: B:K.116, B:K.116, B:D.137, A:K.455, A:K.455, D:K.523, D:K.523 pi-Cation interactions: A:R.451 T8T.3: 17 residues within 4Å: Chain A: V.117, I.118, N.119, H.125 Chain B: V.156, F.157, R.372, H.376, K.377, V.378 Chain C: R.333, F.337, R.352, K.354, N.358, K.523 Ligands: T8T.4 18 PLIP interactions: 9 interactions with chain C, 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: C:R.333, C:K.354, C:N.358, B:V.156, B:R.372, A:N.119, A:N.119, A:H.125 Salt bridges: C:R.352, C:K.354, C:K.354, C:K.523, B:H.376, B:K.377 pi-Cation interactions: C:R.333, C:R.333 Hydrophobic interactions: B:V.156, B:F.157 T8T.4: 15 residues within 4Å: Chain A: K.116, V.117, I.118, I.136, D.137, Q.142, R.145, F.165 Chain B: Y.155, V.156, V.378, R.451, K.455 Chain C: K.523 Ligands: T8T.3 14 PLIP interactions: 2 interactions with chain C, 7 interactions with chain A, 5 interactions with chain B Salt bridges: C:K.523, C:K.523, A:K.116, A:K.116, A:D.137, B:K.455, B:K.455 Hydrophobic interactions: A:I.118 Hydrogen bonds: A:Q.142, A:R.145, A:R.145, B:R.451, B:R.451 pi-Cation interactions: B:R.451 T8T.5: 13 residues within 4Å: Chain B: Q.149, L.150, R.164, D.207, H.215, D.311, K.312, Y.315, D.319, R.366, H.370, Y.374, Q.375 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.150, B:Y.374 Hydrogen bonds: B:Q.149, B:R.164, B:Y.315, B:Y.315, B:Y.315, B:D.319, B:Q.375 Salt bridges: B:K.312, B:R.366 pi-Stacking: B:H.215, B:H.215, B:Y.374 pi-Cation interactions: B:H.215 T8T.6: 17 residues within 4Å: Chain A: V.156, F.157, R.372, H.376, K.377, V.378 Chain B: V.117, I.118, N.119, H.125 Chain D: R.333, F.337, R.352, K.354, N.358, K.523 Ligands: T8T.2 18 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B, 9 interactions with chain D Hydrophobic interactions: A:V.156, A:F.157 Hydrogen bonds: A:V.156, A:R.372, B:N.119, B:N.119, B:H.125, D:R.333, D:K.354, D:N.358 Salt bridges: A:H.376, A:K.377, D:R.352, D:K.354, D:K.354, D:K.523 pi-Cation interactions: D:R.333, D:R.333 T8T.7: 17 residues within 4Å: Chain A: R.333, F.337, R.352, K.354, N.358, K.523 Chain C: V.117, I.118, N.119, H.125 Chain D: V.156, F.157, R.372, H.376, K.377, V.378 Ligands: T8T.11 19 PLIP interactions: 7 interactions with chain D, 9 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: D:V.156, D:F.157 Hydrogen bonds: D:V.156, D:R.372, A:R.333, A:K.354, A:N.358, C:N.119, C:N.119, C:H.125 Salt bridges: D:H.376, D:K.377, D:K.377, A:R.352, A:K.354, A:K.354, A:K.523 pi-Cation interactions: A:R.333, A:R.333 T8T.8: 16 residues within 4Å: Chain B: K.523 Chain C: Y.155, V.156, K.377, V.378, R.451, K.455 Chain D: K.116, V.117, I.118, I.136, D.137, Q.142, R.145, F.165 Ligands: T8T.10 15 PLIP interactions: 7 interactions with chain D, 6 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: D:I.118 Hydrogen bonds: D:Q.142, D:R.145, D:R.145, C:R.451, C:R.451 Salt bridges: D:K.116, D:K.116, D:D.137, C:K.377, C:K.455, C:K.455, B:K.523, B:K.523 pi-Cation interactions: C:R.451 T8T.9: 13 residues within 4Å: Chain C: Q.149, L.150, R.164, D.207, H.215, D.311, K.312, Y.315, D.319, R.366, H.370, Y.374, Q.375 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:L.150, C:Y.374 Hydrogen bonds: C:Q.149, C:R.164, C:Y.315, C:Y.315, C:D.319, C:Q.375 Salt bridges: C:K.312, C:R.366 pi-Stacking: C:H.215, C:H.215, C:Y.374 pi-Cation interactions: C:H.215 T8T.10: 17 residues within 4Å: Chain B: R.333, F.337, R.352, K.354, N.358, K.523 Chain C: V.156, F.157, R.372, H.376, K.377, V.378 Chain D: V.117, I.118, N.119, H.125 Ligands: T8T.8 19 PLIP interactions: 7 interactions with chain C, 9 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: C:V.156, C:F.157 Hydrogen bonds: C:V.156, C:R.372, B:R.333, B:K.354, B:N.358, D:N.119, D:N.119, D:H.125 Salt bridges: C:H.376, C:K.377, C:K.377, B:R.352, B:K.354, B:K.354, B:K.523 pi-Cation interactions: B:R.333, B:R.333 T8T.11: 16 residues within 4Å: Chain A: K.523 Chain C: K.116, V.117, I.118, I.136, D.137, Q.142, R.145, F.165 Chain D: Y.155, V.156, K.377, V.378, R.451, K.455 Ligands: T8T.7 15 PLIP interactions: 6 interactions with chain D, 7 interactions with chain C, 2 interactions with chain A Hydrogen bonds: D:R.451, D:R.451, C:Q.142, C:R.145, C:R.145 Salt bridges: D:K.377, D:K.455, D:K.455, C:K.116, C:K.116, C:D.137, A:K.523, A:K.523 pi-Cation interactions: D:R.451 Hydrophobic interactions: C:I.118 T8T.12: 13 residues within 4Å: Chain D: Q.149, L.150, R.164, D.207, H.215, D.311, K.312, Y.315, D.319, R.366, H.370, Y.374, Q.375 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:L.150, D:Y.374 Hydrogen bonds: D:Q.149, D:R.164, D:Y.315, D:Y.315, D:D.319, D:Q.375 Salt bridges: D:K.312, D:R.366 pi-Stacking: D:H.215, D:H.215, D:Y.374 pi-Cation interactions: D:H.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Orris, B. et al., Phosphorylation of SAMHD1 Thr592 increases C-terminal domain dynamics, tetramer dissociation and ssDNA binding kinetics. Nucleic Acids Res. (2022)

Release Date

2022-07-20

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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