SMTL ID : 4rxs.1

The structure of GTP-dTTP-bound SAMHD1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

GTP.1: 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: TTP.3, MG.6 19 PLIP interactions: 5 interactions with chain A, 12 interactions with chain B, 2 interactions with chain C Water bridges: A:K.368, 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 Hydrogen bonds: B:V.30, B:Q.55, B:R.58 GTP.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, TTP.8 22 PLIP interactions: 12 interactions with chain A, 7 interactions with chain B, 3 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:Q.55, B:K.368, B:Y.369, D:K.436 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.9: 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: TTP.11, MG.14 18 PLIP interactions: 11 interactions with chain D, 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: D:V.30, D:Q.55, D:R.58 Water bridges: D:K.29, D:K.29, D:K.29, D:Q.55, 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 GTP.12: 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.13, TTP.16 23 PLIP interactions: 3 interactions with chain B, 13 interactions with chain C, 7 interactions with chain D Water bridges: B:K.436, C:K.29, C:K.29, C:K.29, C:K.29, C:D.50, C:Q.55, D:K.368, D:Y.369 Salt bridges: B:K.436, B:K.436, C:K.29, C:K.29, C:K.29, C:D.50, D:R.364, D:K.368, D:K.368 Hydrogen bonds: C:V.30, C:Q.55, C:R.58, D:R.364 pi-Cation interactions: D:R.364

8 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.2: 16 residues within 4Å: Chain A: Q.62, L.63, R.77, H.80, H.119, D.120, H.123, H.128, H.146, E.147, D.224, Y.228, D.232, H.283, Y.287, Q.288 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.63, A:Y.287 Hydrogen bonds: A:Q.62, A:R.77, A:E.147, A:D.224, A:Y.228, A:Q.288 Water bridges: A:Q.62, A:H.75, A:H.128, A:H.128, A:Y.287 Salt bridges: A:R.77, A:H.119, A:H.123, A:H.128, A:H.128, A:H.128, A:H.146, A:H.146 TTP.3: 18 residues within 4Å: Chain A: V.69, F.70, 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.1, MG.6 25 PLIP interactions: 9 interactions with chain A, 14 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: A:V.69, A:F.70 Water bridges: A:K.290, A:K.290, C:R.265, C:K.267, C:K.267, C:K.436, C:K.436 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, B:N.32, B:N.32 pi-Cation interactions: C:R.246 TTP.7: 15 residues within 4Å: Chain B: Q.62, L.63, R.77, H.80, H.119, D.120, H.123, H.128, H.146, D.224, Y.228, D.232, H.283, Y.287, Q.288 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.63, B:Y.287 Hydrogen bonds: B:Q.62, B:R.77, B:D.224, B:Y.228, B:Q.288 Water bridges: B:E.147, B:Y.287 Salt bridges: B:R.77, B:H.119, B:H.123, B:H.128, B:H.128, B:H.128, B:H.146, B:H.146 pi-Stacking: B:H.128 TTP.8: 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: GTP.4, MG.5 23 PLIP interactions: 2 interactions with chain A, 13 interactions with chain D, 8 interactions with chain B Hydrogen bonds: A:N.32, A:N.32, D:R.246, D:N.271 Water bridges: D:K.267, D:K.267, D:K.436, D:K.436, 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 Hydrophobic interactions: B:V.69, B:F.70 TTP.10: 16 residues within 4Å: Chain C: Q.62, L.63, R.77, H.80, H.119, D.120, H.123, H.128, H.146, E.147, D.224, Y.228, D.232, H.283, Y.287, Q.288 18 PLIP interactions: 18 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:Q.62, C:H.75, C:Y.287 Salt bridges: C:R.77, C:H.119, C:H.123, C:H.128, C:H.128, C:H.128, C:H.146, C:H.146 TTP.11: 18 residues within 4Å: Chain A: R.246, F.250, R.265, K.267, N.271, K.436 Chain C: V.69, F.70, R.285, H.289, K.290, V.291 Chain D: V.30, I.31, N.32, H.38 Ligands: GTP.9, MG.14 25 PLIP interactions: 14 interactions with chain A, 9 interactions with chain C, 2 interactions with chain D Hydrogen bonds: A:R.246, A:N.271, D:N.32, D:N.32 Water bridges: A:R.265, A:K.267, A:K.267, A:K.436, A:K.436, C:K.290, C:K.290 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 Hydrophobic interactions: C:V.69, C:F.70 TTP.15: 15 residues within 4Å: Chain D: Q.62, L.63, R.77, H.80, H.119, D.120, H.123, H.128, H.146, D.224, Y.228, D.232, H.283, Y.287, Q.288 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:L.63, D:Y.287 Hydrogen bonds: D:Q.62, D:R.77, D:D.224, D:D.224, D:Q.288 Water bridges: D:E.147, D:Y.287 Salt bridges: D:R.77, D:H.119, D:H.123, D:H.128, D:H.128, D:H.128, D:H.146, D:H.146 pi-Stacking: D:H.128 TTP.16: 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: GTP.12, MG.13 23 PLIP interactions: 8 interactions with chain D, 13 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: D:V.69, D:F.70 Water bridges: D:K.290, B:K.267, B:K.267, B:K.436, B:K.436 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, C:N.32, C:N.32 pi-Cation interactions: B:R.246

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: K.29 Chain D: K.436 Ligands: GTP.4, TTP.8 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: K.29 Ligands: GTP.1, TTP.3 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain B: K.436 Chain C: K.29 Ligands: GTP.12, TTP.16 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain D: K.29 Ligands: GTP.9, TTP.11 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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