SMTL ID : 4rxp.1

The structure of GTP-dATP-bound SAMHD1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

DTP.1: 13 residues within 4Å: Chain A: Q.62, L.63, R.77, H.119, H.128, D.224, K.225, Y.228, D.232, R.279, H.283, Y.287, Q.288 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:L.63, A:Y.287 Hydrogen bonds: A:Q.62, A:R.77, A:E.147, A:E.147, A:Y.228, A:Q.288 Water bridges: A:H.128, A:R.133, A:Q.288, A:N.293, A:N.293, A:N.293, A:D.296 Salt bridges: A:H.128, A:H.128, A:H.146, A:K.225, A:R.279, A:R.279, A:H.283 DTP.2: 19 residues within 4Å: Chain A: V.69, F.70, I.238, R.285, H.289, K.290, V.291 Chain B: V.30, I.31, N.32, H.38 Chain C: R.246, F.250, R.265, K.267, N.271, K.436 Ligands: GTP.5, MG.6 21 PLIP interactions: 8 interactions with chain A, 11 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: A:V.69, A:F.70 Water bridges: A:K.290 Salt bridges: A:H.289, A:H.289, A:K.290, A:K.290, A:K.290, C:R.246, C:R.265, C:K.267, C:K.267, C:K.267, C:K.436 Hydrogen bonds: C:R.246, C:N.271, C:N.271, B:N.32, B:N.32 pi-Cation interactions: C:R.246, C:R.246 DTP.7: 12 residues within 4Å: Chain B: Q.62, L.63, R.77, H.128, D.224, K.225, Y.228, D.232, R.279, H.283, Y.287, Q.288 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:L.63, B:Y.287 Hydrogen bonds: B:Q.62, B:R.77, B:Y.228, B:Q.288 Water bridges: B:H.128, B:R.133, B:H.146, B:Q.288, B:N.293, B:N.293, B:N.293, B:D.296 Salt bridges: B:H.128, B:K.225, B:R.279, B:R.279, B:H.283 DTP.8: 19 residues within 4Å: Chain A: V.30, I.31, N.32, H.38 Chain B: V.69, F.70, I.238, R.285, H.289, K.290, V.291 Chain D: R.246, F.250, R.265, K.267, N.271, K.436 Ligands: GTP.3, MG.4 22 PLIP interactions: 13 interactions with chain D, 7 interactions with chain B, 2 interactions with chain A 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 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.9: 13 residues within 4Å: Chain C: Q.62, L.63, R.77, H.119, H.128, 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:R.77, C:E.147, C:D.224, C:Q.288 Water bridges: C:H.128, C:R.133, C:Q.288, C:N.293, C:N.293, C:N.293, C:D.296 Salt bridges: C:H.128, C:H.128, C:H.146, C:K.225, C:R.279, C:R.279, C:H.283 DTP.10: 19 residues within 4Å: Chain A: R.246, F.250, R.265, K.267, N.271, K.436 Chain C: V.69, F.70, I.238, R.285, H.289, K.290, V.291 Chain D: V.30, I.31, N.32, H.38 Ligands: GTP.13, MG.14 21 PLIP interactions: 11 interactions with chain A, 8 interactions with chain C, 2 interactions with chain D Hydrogen bonds: A:R.246, A:N.271, A:N.271, D:N.32, D:N.32 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 Water bridges: C:K.290 DTP.15: 12 residues within 4Å: Chain D: Q.62, L.63, R.77, H.128, D.224, K.225, Y.228, D.232, R.279, H.283, Y.287, Q.288 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:L.63, D:Y.287 Hydrogen bonds: D:Q.62, D:R.77, D:Q.288 Water bridges: D:H.128, D:R.133, D:H.146, D:D.224, D:D.224, D:Q.288, D:N.293, D:N.293, D:N.293, D:D.296 Salt bridges: D:H.128, D:K.225, D:R.279, D:R.279, D:H.283 DTP.16: 19 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, I.238, R.285, H.289, K.290, V.291 Ligands: GTP.11, MG.12 23 PLIP interactions: 7 interactions with chain D, 14 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: D:V.69, D:F.70 Salt bridges: D:H.289, D:H.289, D:K.290, D:K.290, D:K.290, B:R.246, B:R.265, B:K.267, B:K.267, B:K.267, B:K.436 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 pi-Cation interactions: B:R.246, B:R.246

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

GTP.3: 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.4, DTP.8 22 PLIP interactions: 12 interactions with chain A, 8 interactions with chain B, 2 interactions with chain D Hydrogen bonds: A:V.30, A:Q.55, A:R.58, B:R.364 Water bridges: A:K.29, A:K.29, A:K.29, A:K.29, A:K.29, B:K.368, B:K.368, B:Y.369 Salt bridges: A:K.29, A:K.29, A:K.29, A:D.50, B:R.364, B:K.368, B:K.368, D:K.436, D:K.436 pi-Cation interactions: B:R.364 GTP.5: 16 residues within 4Å: Chain A: Y.68, V.69, 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: DTP.2, MG.6 23 PLIP interactions: 8 interactions with chain A, 13 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:R.364, B:V.30, B:Q.55, B:R.58 Water bridges: A:K.368, A:K.368, A:K.368, B:K.29, B:K.29, B:K.29, B:K.29, B:D.50, B:Q.55 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 GTP.11: 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.12, DTP.16 23 PLIP interactions: 13 interactions with chain C, 8 interactions with chain D, 2 interactions with chain B Hydrogen bonds: C:V.30, C:Q.55, C:R.58, D:R.364 Water bridges: C:K.29, C:K.29, C:K.29, C:K.29, C:K.29, C:D.50, D:K.368, D:K.368, D:Y.369 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 GTP.13: 16 residues within 4Å: Chain A: K.436 Chain C: Y.68, V.69, 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: DTP.10, MG.14 22 PLIP interactions: 12 interactions with chain D, 8 interactions with chain C, 2 interactions with chain A Hydrogen bonds: D:V.30, D:Q.55, D:R.58, C:R.364 Water bridges: D:K.29, D:K.29, D:K.29, D:K.29, D:Q.55, C:K.368, C:K.368, C:K.368 Salt bridges: D:K.29, D:K.29, D:K.29, D:D.50, C:R.364, C:K.368, C:K.368, A:K.436, A:K.436 pi-Cation interactions: C:R.364

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: K.29 Chain D: K.436 Ligands: GTP.3, DTP.8 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain B: K.29 Chain C: K.436 Ligands: DTP.2, GTP.5 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain B: K.436 Chain C: K.29 Ligands: GTP.11, DTP.16 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain A: K.436 Chain D: K.29 Ligands: DTP.10, GTP.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, C.F. et al., The mechanism of substrate-controlled allosteric regulation of SAMHD1 activated by GTP. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-03-11

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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