SMTL ID : 4to3.1

Structural basis of cellular dNTP regulation, SAMHD1-dGTP-dGTP-dCTP complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.1: 17 residues within 4Å: Chain A: Q.37, L.38, R.52, R.94, N.95, H.98, H.103, H.121, D.199, K.200, Y.203, D.207, R.254, H.258, Y.262, Q.263 Ligands: MG.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:L.38, A:Y.262 Hydrogen bonds: A:Q.37, A:R.52, A:Y.203, A:D.207, A:Q.263 Water bridges: A:R.94, A:R.94, A:R.254, A:R.254, A:R.254, A:H.258, A:Y.262, A:Y.262, A:Q.263 Salt bridges: A:R.52, A:R.94, A:H.98, A:H.103, A:H.103, A:H.121, A:H.121, A:K.200, A:R.254 pi-Stacking: A:H.103 DCP.7: 17 residues within 4Å: Chain B: Q.37, L.38, R.52, R.94, N.95, H.98, H.103, H.121, D.199, K.200, Y.203, D.207, R.254, H.258, Y.262, Q.263 Ligands: MG.8 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:L.38, B:Y.262 Hydrogen bonds: B:Q.37, B:R.52, B:Y.203, B:D.207, B:Y.262, B:Q.263 Water bridges: B:R.94, B:R.94, B:D.199, B:K.200, B:K.200, B:R.254, B:R.254, B:D.271, B:D.271 Salt bridges: B:R.52, B:R.94, B:H.98, B:H.103, B:H.103, B:H.121, B:H.121, B:K.200, B:R.254 pi-Stacking: B:H.103 DCP.14: 17 residues within 4Å: Chain C: Q.37, L.38, R.52, R.94, N.95, H.98, H.103, H.121, D.199, K.200, Y.203, D.207, R.254, H.258, Y.262, Q.263 Ligands: MG.15 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:L.38, C:Y.262 Hydrogen bonds: C:Q.37, C:R.52, C:Y.203, C:D.207, C:Q.263 Water bridges: C:R.94, C:R.94, C:R.94, C:R.94, C:R.254, C:R.254, C:Y.262, C:Y.262, C:Q.263 Salt bridges: C:R.52, C:R.94, C:H.98, C:H.103, C:H.103, C:H.121, C:H.121, C:K.200, C:R.254 pi-Stacking: C:H.103 DCP.18: 17 residues within 4Å: Chain D: Q.37, L.38, R.52, R.94, N.95, H.98, H.103, H.121, D.199, K.200, Y.203, D.207, R.254, H.258, Y.262, Q.263 Ligands: MG.19 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:L.38, D:Y.262 Hydrogen bonds: D:Q.37, D:R.52, D:D.207, D:Y.262, D:Q.263 Water bridges: D:R.94, D:R.94, D:R.94, D:R.94, D:R.94, D:R.94 Salt bridges: D:R.52, D:R.94, D:H.98, D:H.103, D:H.121, D:H.121, D:K.200, D:R.254 pi-Stacking: D:H.103

8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 2 residues within 4Å: Chain A: K.200 Ligands: DCP.1 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain A: K.411 Chain B: K.4 Ligands: DGT.4, DGT.10 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain A: K.4 Chain B: K.411 Ligands: DGT.11, DGT.20 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: R.94, K.200 Ligands: DCP.7 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain C: K.4 Ligands: DGT.9, DGT.17 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Ligands: DCP.14 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain C: K.411 Chain D: K.4 Ligands: DGT.3, DGT.12 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain D: K.200 Ligands: DCP.18 No protein-ligand interaction detected (PLIP)

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

DGT.3: 16 residues within 4Å: Chain A: Y.43, V.44, V.266, R.339, K.343 Chain C: K.411 Chain D: K.4, V.5, I.6, I.24, D.25, Q.30, R.33, F.53 Ligands: DGT.12, MG.16 21 PLIP interactions: 8 interactions with chain A, 11 interactions with chain D, 2 interactions with chain C Hydrogen bonds: A:R.339, D:Q.30, D:R.33 Water bridges: A:K.343, A:K.343, A:K.343, D:K.4, D:K.4, D:K.4, D:K.4 Salt bridges: A:R.339, A:K.343, A:K.343, D:K.4, D:K.4, D:K.4, D:D.25, C:K.411, C:K.411 pi-Cation interactions: A:R.339 Hydrophobic interactions: D:I.6 DGT.4: 21 residues within 4Å: Chain A: D.218, R.221, F.225, R.240, K.242, N.246, K.411 Chain B: V.5, I.6, N.7, H.13 Chain C: V.44, F.45, G.212, I.213, R.260, H.264, K.265, V.266 Ligands: MG.5, DGT.10 24 PLIP interactions: 2 interactions with chain B, 8 interactions with chain C, 14 interactions with chain A Hydrogen bonds: B:N.7, B:N.7, A:R.221, A:N.246 Hydrophobic interactions: C:V.44, C:F.45 Water bridges: C:R.260, A:R.221, A:R.221, A:N.246 Salt bridges: C:H.264, C:H.264, C:K.265, C:K.265, C:K.265, A:D.218, A:R.221, A:R.240, A:K.242, A:K.242, A:K.242, A:K.411 pi-Cation interactions: A:R.221, A:R.221 DGT.9: 16 residues within 4Å: Chain B: Y.43, V.44, V.266, R.339, K.343 Chain C: K.4, V.5, I.6, I.24, D.25, Q.30, R.33, F.53 Chain D: K.411 Ligands: MG.13, DGT.17 16 PLIP interactions: 9 interactions with chain C, 2 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: C:I.6 Hydrogen bonds: C:Q.30, C:R.33, B:R.339 Water bridges: C:K.4, C:K.4 Salt bridges: C:K.4, C:K.4, C:K.4, C:D.25, D:K.411, D:K.411, B:R.339, B:K.343, B:K.343 pi-Cation interactions: B:R.339 DGT.10: 16 residues within 4Å: Chain A: K.411 Chain B: K.4, V.5, I.6, I.24, D.25, Q.30, R.33, F.53 Chain C: Y.43, V.44, V.266, R.339, K.343 Ligands: DGT.4, MG.5 20 PLIP interactions: 6 interactions with chain C, 12 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:R.339, B:Q.30, B:R.33 Water bridges: C:K.343, B:K.4, B:K.4, B:K.4, B:D.25, B:Q.30 Salt bridges: C:R.339, C:K.343, C:K.343, B:K.4, B:K.4, B:K.4, B:D.25, A:K.411, A:K.411 pi-Cation interactions: C:R.339 Hydrophobic interactions: B:I.6 DGT.11: 21 residues within 4Å: Chain A: V.5, I.6, N.7, H.13 Chain B: D.218, R.221, F.225, R.240, K.242, N.246, K.411 Chain D: V.44, F.45, G.212, I.213, R.260, H.264, K.265, V.266 Ligands: MG.6, DGT.20 23 PLIP interactions: 13 interactions with chain B, 8 interactions with chain D, 2 interactions with chain A Hydrogen bonds: B:R.221, B:N.246, A:N.7, A:N.7 Water bridges: B:D.218, B:N.246, D:R.260 Salt bridges: B:D.218, B:R.221, B:R.240, B:K.242, B:K.242, B:K.242, B:K.411, D:H.264, D:H.264, D:K.265, D:K.265, D:K.265 pi-Cation interactions: B:R.221, B:R.221 Hydrophobic interactions: D:V.44, D:F.45 DGT.12: 21 residues within 4Å: Chain A: V.44, F.45, G.212, I.213, R.260, H.264, K.265, V.266 Chain C: D.218, R.221, F.225, R.240, K.242, N.246, K.411 Chain D: V.5, I.6, N.7, H.13 Ligands: DGT.3, MG.16 22 PLIP interactions: 8 interactions with chain A, 12 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: A:V.44, A:F.45 Water bridges: A:R.260, C:N.246 Salt bridges: A:H.264, A:H.264, A:K.265, A:K.265, A:K.265, C:R.221, C:R.240, C:K.242, C:K.242, C:K.242, C:K.411 Hydrogen bonds: C:D.218, C:R.221, C:N.246, D:N.7, D:N.7 pi-Cation interactions: C:R.221, C:R.221 DGT.17: 21 residues within 4Å: Chain B: V.44, F.45, G.212, I.213, R.260, H.264, K.265, V.266 Chain C: V.5, I.6, N.7, H.13 Chain D: D.218, R.221, F.225, R.240, K.242, N.246, K.411 Ligands: DGT.9, MG.13 26 PLIP interactions: 16 interactions with chain D, 2 interactions with chain C, 8 interactions with chain B Hydrogen bonds: D:R.221, D:N.246, C:N.7, C:N.7 Water bridges: D:R.240, D:R.240, D:K.242, D:K.242, D:N.246, B:R.260 Salt bridges: D:D.218, D:R.221, D:R.240, D:K.242, D:K.242, D:K.242, D:K.411, B:H.264, B:H.264, B:K.265, B:K.265, B:K.265 pi-Cation interactions: D:R.221, D:R.221 Hydrophobic interactions: B:V.44, B:F.45 DGT.20: 16 residues within 4Å: Chain A: K.4, V.5, I.6, I.24, D.25, Q.30, R.33, F.53 Chain B: K.411 Chain D: Y.43, V.44, V.266, R.339, K.343 Ligands: MG.6, DGT.11 21 PLIP interactions: 13 interactions with chain A, 6 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: A:I.6 Hydrogen bonds: A:Q.30, A:R.33, D:R.339 Water bridges: A:K.4, A:K.4, A:K.4, A:K.4, A:D.25, A:Q.30, D:K.343 Salt bridges: A:K.4, A:K.4, A:K.4, A:D.25, D:R.339, D:K.343, D:K.343, B:K.411, B:K.411 pi-Cation interactions: D:R.339

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ji, X. et al., Structural basis of cellular dNTP regulation by SAMHD1. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-10-01

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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