SMTL ID : 4mz7.1

Structural insight into dGTP-dependent activation of tetrameric SAMHD1 deoxynucleoside triphosphate triphosphohydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: R.77, H.80, H.119, D.120, D.224 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.80, A:H.119, A:D.120, A:D.224 ZN.8: 5 residues within 4Å: Chain B: R.77, H.80, H.119, D.120, D.224 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.80, B:H.119, B:D.120, B:D.224 ZN.11: 5 residues within 4Å: Chain C: R.77, H.80, H.119, D.120, D.224 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.80, C:H.119, C:D.120, C:D.224 ZN.18: 5 residues within 4Å: Chain D: R.77, H.80, H.119, D.120, D.224 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.80, D:H.119, D:D.120, D:D.224

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

DGT.2: 13 residues within 4Å: Chain A: Q.62, L.63, R.77, H.128, D.222, D.224, K.225, Y.228, D.232, R.279, H.283, Y.287, Q.288 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:L.63, A:Y.287 Hydrogen bonds: A:Q.62, A:L.63, A:R.77, A:D.222, A:D.224, A:Y.228, A:Y.287, A:Q.288 Water bridges: A:H.128, A:S.215, A:R.279, A:R.279 Salt bridges: A:K.225, A:K.225, A:R.279, A:R.279, A:H.283, A:D.296 DGT.3: 21 residues within 4Å: Chain A: V.69, F.70, G.237, I.238, R.285, H.289, K.290, V.291 Chain B: V.30, I.31, N.32, H.38 Chain C: D.243, R.246, F.250, R.265, K.267, N.271, K.436 Ligands: DGT.6, MG.7 27 PLIP interactions: 16 interactions with chain C, 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: C:R.246, C:N.271, A:G.237, B:N.32, B:N.32 Water bridges: C:R.246, C:R.246, C:R.246, C:R.265, C:K.267, C:K.436, A:R.285 Salt bridges: C:R.246, C:R.265, C:K.267, C:K.267, C:K.267, C:K.436, A:H.289, A:H.289, A:K.290, A:K.290, A:K.290 pi-Cation interactions: C:R.246, C:R.246 Hydrophobic interactions: A:V.69, A:F.70 DGT.4: 16 residues within 4Å: Chain A: K.29, V.30, I.31, I.49, D.50, Q.55, R.58, F.78 Chain B: Y.68, V.69, V.291, R.364, K.368 Chain D: K.436 Ligands: MG.5, DTP.10 22 PLIP interactions: 8 interactions with chain B, 10 interactions with chain A, 4 interactions with chain D Hydrogen bonds: B:R.364, A:Q.55, A:R.58 Water bridges: B:K.368, B:K.368, B:Y.369, A:K.29, A:K.29, A:K.29, D:K.436, D:K.436 Salt bridges: B:R.364, B:K.368, B:K.368, A:K.29, A:K.29, A:K.29, A:D.50, D:K.436, D:K.436 pi-Cation interactions: B:R.364 Hydrophobic interactions: A:I.31 DGT.6: 17 residues within 4Å: Chain A: Y.68, V.69, P.71, V.291, R.364, K.368 Chain B: K.29, V.30, I.31, I.49, D.50, Q.55, R.58, F.78 Chain C: K.436 Ligands: DGT.3, MG.7 24 PLIP interactions: 9 interactions with chain A, 11 interactions with chain B, 4 interactions with chain C Hydrogen bonds: A:R.364, B:Q.55, B:R.58 Water bridges: A:K.368, A:K.368, A:K.368, A:Y.369, B:K.29, B:K.29, B:K.29, B:K.29, C:K.436, C:K.436 Salt bridges: A:R.364, A:K.368, A:K.368, B:K.29, B:K.29, B:K.29, B:D.50, C:K.436, C:K.436 pi-Cation interactions: A:R.364 Hydrophobic interactions: B:I.31 DGT.9: 13 residues within 4Å: Chain B: Q.62, L.63, R.77, H.128, D.222, D.224, K.225, Y.228, D.232, R.279, H.283, Y.287, Q.288 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:L.63, B:Y.287 Hydrogen bonds: B:Q.62, B:L.63, B:R.77, B:D.222, B:D.224, B:Y.228, B:Y.287, B:Q.288 Water bridges: B:H.128, B:R.133, B:E.147, B:K.217, B:K.225, B:R.279, B:R.279, B:H.283 Salt bridges: B:K.225, B:K.225, B:R.279, B:R.279, B:H.283, B:D.296 DGT.12: 13 residues within 4Å: Chain C: Q.62, L.63, R.77, H.128, D.222, D.224, K.225, Y.228, D.232, R.279, H.283, Y.287, Q.288 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:L.63, C:Y.287 Hydrogen bonds: C:Q.62, C:L.63, C:R.77, C:D.222, C:D.224, C:Y.287, C:Q.288 Water bridges: C:H.128, C:H.128, C:H.128, C:S.215, C:R.279, C:R.279 Salt bridges: C:K.225, C:K.225, C:R.279, C:R.279, C:H.283, C:D.296 DGT.13: 21 residues within 4Å: Chain A: D.243, R.246, F.250, R.265, K.267, N.271, K.436 Chain C: V.69, F.70, G.237, I.238, R.285, H.289, K.290, V.291 Chain D: V.30, I.31, N.32, H.38 Ligands: DGT.16, MG.17 28 PLIP interactions: 2 interactions with chain D, 17 interactions with chain A, 9 interactions with chain C Hydrogen bonds: D:N.32, D:N.32, A:D.243, A:R.246, A:N.271, C:G.237 Water bridges: A:R.246, A:R.265, A:K.267, A:E.268, A:E.268, A:K.436, C:R.285 Salt bridges: A:R.246, A:R.265, A:K.267, A:K.267, A:K.267, A:K.436, C:H.289, C:H.289, C:K.290, C:K.290, C:K.290 pi-Cation interactions: A:R.246, A:R.246 Hydrophobic interactions: C:V.69, C:F.70 DGT.14: 16 residues within 4Å: Chain B: K.436 Chain C: K.29, V.30, I.31, I.49, D.50, Q.55, R.58, F.78 Chain D: Y.68, V.69, V.291, R.364, K.368 Ligands: MG.15, DTP.20 22 PLIP interactions: 10 interactions with chain C, 8 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: C:I.31 Hydrogen bonds: C:Q.55, C:R.58, D:R.364 Water bridges: C:K.29, C:K.29, C:K.29, D:K.368, D:K.368, D:Y.369, B:K.436, B:K.436 Salt bridges: C:K.29, C:K.29, C:K.29, C:D.50, D:R.364, D:K.368, D:K.368, B:K.436, B:K.436 pi-Cation interactions: D:R.364 DGT.16: 17 residues within 4Å: Chain A: K.436 Chain C: Y.68, V.69, P.71, V.291, R.364, K.368 Chain D: K.29, V.30, I.31, I.49, D.50, Q.55, R.58, F.78 Ligands: DGT.13, MG.17 24 PLIP interactions: 9 interactions with chain C, 11 interactions with chain D, 4 interactions with chain A Hydrogen bonds: C:R.364, D:Q.55, D:R.58 Water bridges: C:K.368, C:K.368, C:K.368, C:Y.369, D:K.29, D:K.29, D:K.29, D:K.29, A:K.436, A:K.436 Salt bridges: C:R.364, C:K.368, C:K.368, D:K.29, D:K.29, D:K.29, D:D.50, A:K.436, A:K.436 pi-Cation interactions: C:R.364 Hydrophobic interactions: D:I.31 DGT.19: 13 residues within 4Å: Chain D: Q.62, L.63, R.77, H.128, D.222, D.224, K.225, Y.228, D.232, R.279, H.283, Y.287, Q.288 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:L.63, D:Y.287 Hydrogen bonds: D:Q.62, D:L.63, D:R.77, D:D.222, D:D.224, D:Y.287, D:Q.288 Water bridges: D:H.128, D:R.133, D:K.217, D:K.225, D:R.279, D:R.279, D:H.283 Salt bridges: D:K.225, D:K.225, D:R.279, D:R.279, D:H.283, D:D.296

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: K.29 Chain D: K.436 Ligands: DGT.4, DTP.10 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: K.29 Chain C: K.436 Ligands: DGT.3, DGT.6 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain B: K.436 Chain C: K.29 Ligands: DGT.14, DTP.20 No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain A: K.436 Chain D: K.29 Ligands: DGT.13, DGT.16 No protein-ligand interaction detected (PLIP)

2 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.10: 18 residues within 4Å: Chain A: V.30, I.31, N.32, H.38 Chain B: V.69, F.70, R.285, H.289, K.290, V.291 Chain D: R.246, F.250, R.265, K.267, N.271, K.436 Ligands: DGT.4, MG.5 28 PLIP interactions: 18 interactions with chain D, 2 interactions with chain A, 8 interactions with chain B Hydrogen bonds: D:R.246, D:N.271, D:N.271, A:N.32, A:N.32 Water bridges: D:R.246, D:R.246, D:R.246, D:R.246, D:R.265, D:K.267, D:K.267, B:K.290 Salt bridges: D:R.246, D:R.265, D:K.267, D:K.267, D:K.267, D:K.436, B:H.289, B:H.289, B:K.290, B:K.290, B:K.290 pi-Cation interactions: D:R.246, D:R.246 Hydrophobic interactions: B:V.69, B:F.70 DTP.20: 18 residues within 4Å: Chain B: R.246, F.250, R.265, K.267, N.271, K.436 Chain C: V.30, I.31, N.32, H.38 Chain D: V.69, F.70, R.285, H.289, K.290, V.291 Ligands: DGT.14, MG.15 29 PLIP interactions: 19 interactions with chain B, 8 interactions with chain D, 2 interactions with chain C Hydrogen bonds: B:R.246, B:N.271, B:N.271, C:N.32, C:N.32 Water bridges: B:D.243, B:R.246, B:R.246, B:R.246, B:R.246, B:R.265, B:K.267, B:K.267, D:K.290 Salt bridges: B:R.246, B:R.265, B:K.267, B:K.267, B:K.267, B:K.436, D:H.289, D:H.289, D:K.290, D:K.290, D:K.290 pi-Cation interactions: B:R.246, B:R.246 Hydrophobic interactions: D:V.69, D:F.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, C. et al., Structural insight into dGTP-dependent activation of tetrameric SAMHD1 deoxynucleoside triphosphate triphosphohydrolase. Nat Commun (2013)

Release Date

2013-11-20

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

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