SMTL ID : 7lu5.2 (3 other biounits)

SAMHD1(113-626) H206R D207N R366H

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.57 Å

Oligo State

homo-tetramer

Ligands

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

DGT.1: 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, L.362, K.364 Ligands: DGT.4 15 PLIP interactions: 6 interactions with chain D, 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: D:R.360, A:Q.51, A:R.54 Salt bridges: D:K.286, D:R.360, D:K.364, D:K.364, A:K.25, A:K.25, A:K.25, A:D.46, B:K.432, B:K.432 pi-Cation interactions: D:R.360 Hydrophobic interactions: A:I.27 DGT.2: 18 residues within 4Å: Chain A: D.239, R.242, 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, R.281, H.285, K.286, V.287 Ligands: DGT.5 19 PLIP interactions: 9 interactions with chain C, 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:V.65, C:F.66 Hydrogen bonds: C:G.233, C:R.281, A:R.242, A:N.267, B:N.28, B:N.28 Salt bridges: C:H.285, C:H.285, C:K.286, C:K.286, C:K.286, A:R.242, A:R.261, A:K.263, A:K.432 pi-Cation interactions: A:R.242, A:R.242 DGT.3: 16 residues within 4Å: Chain A: Y.64, V.65, K.286, V.287, R.360, L.362, K.364 Chain C: K.432 Chain D: K.25, V.26, I.27, D.46, Q.51, R.54, F.74 Ligands: DGT.7 12 PLIP interactions: 1 interactions with chain C, 7 interactions with chain D, 4 interactions with chain A Salt bridges: C:K.432, D:K.25, D:K.25, D:K.25, D:D.46, A:K.286, A:R.360, A:K.364, A:K.364 Hydrophobic interactions: D:I.27 Hydrogen bonds: D:Q.51, D:R.54 DGT.4: 15 residues within 4Å: Chain A: V.26, I.27, N.28 Chain B: R.242, F.246, R.261, K.263, N.267, K.432 Chain D: V.65, F.66, R.281, H.285, K.286 Ligands: DGT.1 17 PLIP interactions: 11 interactions with chain B, 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: B:R.242, B:R.242, B:N.267, D:R.281, A:N.28, A:N.28 Salt bridges: B:R.261, B:R.261, B:K.263, B:K.263, B:K.263, B:K.432, D:K.286, D:K.286 pi-Cation interactions: B:R.242, B:R.242 Hydrophobic interactions: D:V.65 DGT.5: 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, P.67, V.287, R.360, K.364 Ligands: DGT.2 14 PLIP interactions: 7 interactions with chain B, 5 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: B:I.27 Hydrogen bonds: B:Q.51, B:R.54 Salt bridges: B:K.25, B:K.25, B:K.25, B:D.46, C:K.286, C:R.360, C:K.364, C:K.364, A:K.432, A:K.432 pi-Cation interactions: C:R.360 DGT.6: 16 residues within 4Å: Chain B: Y.64, V.65, V.287, R.360, L.362, 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: DGT.8 13 PLIP interactions: 7 interactions with chain C, 4 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: C:I.27 Hydrogen bonds: C:Q.51, C:R.54, B:R.360 Salt bridges: C:K.25, C:K.25, C:K.25, C:D.46, B:R.360, B:K.364, D:K.432, D:K.432 pi-Cation interactions: B:R.360 DGT.7: 17 residues within 4Å: Chain A: V.65, F.66, I.234, R.281, H.285, K.286, V.287 Chain C: D.239, R.242, R.261, K.263, N.267, K.432 Chain D: V.26, N.28, H.34 Ligands: DGT.3 21 PLIP interactions: 7 interactions with chain A, 12 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: A:V.65, A:F.66 Salt bridges: A:H.285, A:H.285, A:K.286, A:K.286, A:K.286, C:R.242, C:R.261, C:K.263, C:K.263, C:K.263, C:K.432 Hydrogen bonds: C:D.239, C:D.239, C:R.242, C:N.267, D:N.28, D:N.28 pi-Cation interactions: C:R.242, C:R.242 DGT.8: 17 residues within 4Å: Chain B: V.65, F.66, R.281, H.285, K.286, V.287 Chain C: V.26, I.27, N.28, H.34 Chain D: R.242, F.246, R.261, K.263, N.267, K.432 Ligands: DGT.6 17 PLIP interactions: 3 interactions with chain C, 11 interactions with chain D, 3 interactions with chain B Hydrogen bonds: C:V.26, C:N.28, C:N.28, D:R.242, D:R.242, D:R.261, D:N.267 Salt bridges: D:R.242, D:K.263, D:K.263, D:K.432, D:K.432, B:H.285, B:K.286 pi-Cation interactions: D:R.242, D:R.242 Hydrophobic interactions: B:F.66

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
E

B
F

C
G

D
H

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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