SMTL ID : 4tnx.1

Structure basis of cellular dNTP regulation, SAMHD1-GTP-dGTP complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-tetramer

Ligands

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

DGT.1: 20 residues within 4Å: Chain A: V.44, F.45, G.212, I.213, R.260, H.264, K.265 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: GTP.2, MG.9 22 PLIP interactions: 3 interactions with chain D, 7 interactions with chain A, 12 interactions with chain C Hydrogen bonds: D:N.7, D:N.7, C:R.221, C:N.246 Water bridges: D:K.4, C:K.242 Hydrophobic interactions: A:V.44, A:F.45 Salt bridges: A:H.264, A:H.264, A:K.265, A:K.265, A:K.265, C:D.218, C:R.221, C:R.240, C:K.242, C:K.242, C:K.242, C:K.411 pi-Cation interactions: C:R.221, C:R.221 DGT.8: 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.3, GTP.4 22 PLIP interactions: 8 interactions with chain D, 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: D:V.44, D:F.45 Water bridges: D:R.260, B:R.240 Salt bridges: D:H.264, D:H.264, D:K.265, D:K.265, D:K.265, B:D.218, B:R.221, B:R.240, B:K.242, B:K.242, B:K.242, B:K.411 Hydrogen bonds: B:R.221, B:N.246, A:N.7, A:N.7 pi-Cation interactions: B:R.221, B:R.221 DGT.11: 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.7, GTP.12 20 PLIP interactions: 8 interactions with chain C, 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:V.44, C:F.45 Hydrogen bonds: C:R.260, A:R.221, A:N.246, B:N.7, B:N.7 Salt bridges: C:H.264, C:H.264, C:K.265, C:K.265, C:K.265, 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.13: 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: GTP.6, MG.10 26 PLIP interactions: 10 interactions with chain B, 14 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: B:V.44, B:F.45 Water bridges: B:R.260, B:R.260, B:K.265, B:K.265, D:R.221, D:R.240, D:K.242 Salt bridges: B:H.264, B:H.264, B:K.265, B:K.265, D:D.218, D:R.221, D:R.240, D:K.242, D:K.242, D:K.242, D:K.411 Hydrogen bonds: D:R.221, D:N.246, C:N.7, C:N.7 pi-Cation interactions: D:R.221, D:R.221

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

GTP.2: 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.1, MG.9 20 PLIP interactions: 12 interactions with chain D, 5 interactions with chain A, 3 interactions with chain C Hydrogen bonds: D:V.5, D:Q.30, D:R.33 Water bridges: D:K.4, D:K.4, D:V.5, D:V.5, D:D.25, A:K.343, C:K.411 Salt bridges: D:K.4, D:K.4, D:K.4, D:D.25, A:R.339, A:K.343, A:K.343, C:K.411, C:K.411 pi-Cation interactions: A:R.339 GTP.4: 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.3, DGT.8 17 PLIP interactions: 2 interactions with chain B, 10 interactions with chain A, 5 interactions with chain D Salt bridges: B:K.411, B:K.411, A:K.4, A:K.4, A:K.4, A:D.25, D:R.339, D:K.343, D:K.343 Hydrogen bonds: A:V.5, A:Q.30, A:R.33, D:R.339 Water bridges: A:K.4, A:D.25, A:Q.30 pi-Cation interactions: D:R.339 GTP.6: 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.10, DGT.13 17 PLIP interactions: 9 interactions with chain C, 6 interactions with chain B, 2 interactions with chain D Hydrogen bonds: C:V.5, C:Q.30, C:R.33, B:R.339 Water bridges: C:K.4, C:K.4, B:Y.344 Salt bridges: C:K.4, C:K.4, C:K.4, C:D.25, B:R.339, B:K.343, B:K.343, D:K.411, D:K.411 pi-Cation interactions: B:R.339 GTP.12: 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: MG.7, DGT.11 17 PLIP interactions: 10 interactions with chain B, 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:V.5, B:Q.30, B:R.33 Water bridges: B:K.4, B:K.4, B:V.5, C:R.339 Salt bridges: B:K.4, B:K.4, B:K.4, B:D.25, C:R.339, C:K.343, C:K.343, A:K.411, A:K.411 pi-Cation interactions: C:R.339

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: K.4 Chain B: K.411 Ligands: GTP.4, DGT.8 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain A: K.411 Chain B: K.4 Ligands: DGT.11, GTP.12 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain C: K.411 Chain D: K.4 Ligands: DGT.1, GTP.2 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain C: K.4 Ligands: GTP.6, DGT.13 No protein-ligand interaction detected (PLIP)

1 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.5: 10 residues within 4Å: Chain A: R.52, R.94, N.95, H.98, H.103, H.121, D.199, K.200, Y.203, R.254 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.95, A:H.258 Water bridges: A:R.52, A:R.52, A:R.94, A:N.95, A:K.200, A:K.200 Salt bridges: A:R.52, A:R.94, A:R.94, A:H.98, A:H.103, A:H.103, A:H.121, A:H.121, A:K.200, A:R.254

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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