SMTL ID : 7ltt.1

SAMHD1(113-626) H206R D207N R366C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

DGT.1: 16 residues within 4Å: Chain A: Y.64, V.65, V.287, R.360, K.364 Chain C: K.432 Chain D: K.25, V.26, I.27, I.45, D.46, Q.51, R.54, F.74 Ligands: DGT.8, MG.9 20 PLIP interactions: 11 interactions with chain D, 7 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: D:I.27 Hydrogen bonds: D:Q.51, D:R.54, A:R.360 Water bridges: D:K.25, D:K.25, D:K.25, D:D.46, A:K.286, A:K.364 Salt bridges: D:K.25, D:K.25, D:K.25, D:D.46, A:R.360, A:K.364, A:K.364, C:K.432, C:K.432 pi-Cation interactions: A:R.360 DGT.2: 21 residues within 4Å: Chain A: D.239, R.242, F.246, R.261, K.263, N.267, K.432 Chain B: V.26, I.27, N.28, H.34 Chain C: V.65, F.66, G.233, I.234, R.281, H.285, K.286, V.287 Ligands: MG.5, DGT.6 22 PLIP interactions: 7 interactions with chain C, 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:V.65, C:F.66 Water bridges: C:R.281, A:K.263, A:K.263 Salt bridges: C:H.285, C:H.285, C:K.286, C:K.286, A:D.239, A:R.242, A:R.261, A:K.263, A:K.263, A:K.263, A:K.432 Hydrogen bonds: A:R.242, A:N.267, B:N.28, B:N.28 pi-Cation interactions: A:R.242, A:R.242 DGT.4: 16 residues within 4Å: Chain A: K.25, V.26, I.27, I.45, D.46, Q.51, R.54, F.74 Chain B: K.432 Chain D: Y.64, V.65, V.287, R.360, K.364 Ligands: MG.3, DGT.7 21 PLIP interactions: 12 interactions with chain A, 7 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: A:I.27 Hydrogen bonds: A:Q.51, A:R.54, D:R.360 Water bridges: A:K.25, A:K.25, A:K.25, A:K.25, A:D.46, D:K.364, D:Y.365 Salt bridges: A:K.25, A:K.25, A:K.25, A:D.46, D:R.360, D:K.364, D:K.364, B:K.432, B:K.432 pi-Cation interactions: D:R.360 DGT.6: 16 residues within 4Å: Chain A: K.432 Chain B: K.25, V.26, I.27, I.45, D.46, Q.51, R.54, F.74 Chain C: Y.64, V.65, V.287, R.360, K.364 Ligands: DGT.2, MG.5 19 PLIP interactions: 10 interactions with chain B, 8 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:I.27 Hydrogen bonds: B:Q.51, B:R.54, C:R.360 Water bridges: B:K.25, B:K.25, B:D.46, C:K.364, C:Y.365, C:Y.365 Salt bridges: B:K.25, B:K.25, B:K.25, B:D.46, C:R.360, C:K.364, C:K.364, A:K.432 pi-Cation interactions: C:R.360 DGT.7: 21 residues within 4Å: Chain A: V.26, I.27, N.28, H.34 Chain B: D.239, R.242, F.246, R.261, K.263, N.267, K.432 Chain D: V.65, F.66, G.233, I.234, R.281, H.285, K.286, V.287 Ligands: MG.3, DGT.4 23 PLIP interactions: 13 interactions with chain B, 8 interactions with chain D, 2 interactions with chain A Hydrogen bonds: B:R.242, B:N.267, A:N.28, A:N.28 Water bridges: B:K.263, B:K.263, D:R.281, D:R.281 Salt bridges: B:D.239, B:R.242, B:R.261, B:K.263, B:K.263, B:K.263, B:K.432, D:H.285, D:H.285, D:K.286, D:K.286 pi-Cation interactions: B:R.242, B:R.242 Hydrophobic interactions: D:V.65, D:F.66 DGT.8: 20 residues within 4Å: Chain A: V.65, F.66, G.233, I.234, R.281, H.285, K.286 Chain C: D.239, R.242, F.246, R.261, K.263, N.267, K.432 Chain D: V.26, I.27, N.28, H.34 Ligands: DGT.1, MG.9 26 PLIP interactions: 9 interactions with chain A, 14 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: A:V.65, A:F.66 Water bridges: A:R.281, A:K.286, C:D.239, C:K.263, C:K.263, D:N.28 Salt bridges: A:H.285, A:H.285, A:K.286, A:K.286, A:K.286, C:D.239, C:R.242, C:R.261, C:K.263, C:K.263, C:K.263, C:K.432 Hydrogen bonds: C:R.242, C:N.267, D:N.28, D:N.28 pi-Cation interactions: C:R.242, C:R.242 DGT.11: 17 residues within 4Å: Chain B: Y.64, V.65, K.286, V.287, R.360, K.364 Chain C: K.25, V.26, I.27, I.45, D.46, Q.51, R.54, F.74 Chain D: K.432 Ligands: MG.10, DGT.12 17 PLIP interactions: 1 interactions with chain D, 10 interactions with chain C, 6 interactions with chain B Salt bridges: D:K.432, C:K.25, C:K.25, C:K.25, C:D.46, B:K.286, B:R.360, B:K.364, B:K.364 Hydrophobic interactions: C:I.27 Hydrogen bonds: C:Q.51, C:R.54, B:R.360 Water bridges: C:K.25, C:K.25, C:K.25 pi-Cation interactions: B:R.360 DGT.12: 21 residues within 4Å: Chain B: V.65, F.66, G.233, I.234, R.281, H.285, K.286, V.287 Chain C: V.26, I.27, N.28, H.34 Chain D: D.239, R.242, F.246, R.261, K.263, N.267, K.432 Ligands: MG.10, DGT.11 22 PLIP interactions: 12 interactions with chain D, 2 interactions with chain C, 8 interactions with chain B Hydrogen bonds: D:R.242, D:N.267, C:N.28, C:N.28 Water bridges: D:K.263, D:K.263, B:R.281, B:R.281 Salt bridges: D:R.242, D:R.261, D:K.263, D:K.263, D:K.263, D:K.432, B:H.285, B:H.285, B:K.286, B:K.286 pi-Cation interactions: D:R.242, D:R.242 Hydrophobic interactions: B:V.65, B:F.66

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: K.25 Ligands: DGT.4, DGT.7 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: K.25 Ligands: DGT.2, DGT.6 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain C: K.432 Chain D: K.25 Ligands: DGT.1, DGT.8 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain C: K.25 Chain D: K.432 Ligands: DGT.11, DGT.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bowen, N.E. et al., Structural and functional characterization explains loss of dNTPase activity of the cancer-specific R366C/H mutant SAMHD1 proteins. J.Biol.Chem. (2021)

Release Date

2021-11-24

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