SMTL ID : 7a5y.2 (1 other biounit)

Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with Rp-dGTP-alphaS (T8T) and Mg

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-tetramer

Ligands

4 x FE: FE (III) ION(Non-covalent)

FE.1: 6 residues within 4Å: Chain A: H.61, H.100, D.101, D.205 Ligands: MG.2, T8T.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.61, A:H.100, A:D.101, A:D.205, H2O.1 FE.11: 6 residues within 4Å: Chain B: H.61, H.100, D.101, D.205 Ligands: MG.12, T8T.15 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.61, B:H.100, B:D.101, B:D.205, H2O.2 FE.18: 6 residues within 4Å: Chain C: H.61, H.100, D.101, D.205 Ligands: MG.19, T8T.21 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.61, C:H.100, C:D.101, C:D.205, H2O.4 FE.25: 6 residues within 4Å: Chain D: H.61, H.100, D.101, D.205 Ligands: MG.26, T8T.28 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.61, D:H.100, D:D.101, D:D.205, H2O.5

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

MG.2: 5 residues within 4Å: Chain A: H.100, D.101, H.127 Ligands: FE.1, T8T.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.101, A:H.127, H2O.1, H2O.1, H2O.1 MG.3: 1 residues within 4Å: Ligands: T8T.5 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: K.10 Ligands: T8T.9, T8T.10 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain C: K.10 Ligands: T8T.8, T8T.24 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain B: H.100, D.101, H.127 Ligands: FE.11, T8T.15 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.101, B:H.127, H2O.2, H2O.3, H2O.3 MG.13: 2 residues within 4Å: Chain B: K.206 Ligands: T8T.15 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain B: K.10 Ligands: T8T.6, T8T.23 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain B: K.417 Chain D: K.10 Ligands: T8T.17, T8T.22 No protein-ligand interaction detected (PLIP) MG.19: 6 residues within 4Å: Chain C: H.100, D.101, H.104, H.127 Ligands: FE.18, T8T.21 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.101, C:H.127, H2O.4, H2O.4, H2O.5 MG.20: 3 residues within 4Å: Chain C: D.203, K.206 Ligands: T8T.21 No protein-ligand interaction detected (PLIP) MG.26: 6 residues within 4Å: Chain D: D.101, H.104, H.127, E.128 Ligands: FE.25, T8T.28 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.101, D:H.127, H2O.5, H2O.6, H2O.6 MG.27: 2 residues within 4Å: Chain D: K.206 Ligands: T8T.28 No protein-ligand interaction detected (PLIP)

12 x T8T: 2'-deoxyguanosine-5'-O-(1-thiotriphosphate)(Non-covalent)

T8T.5: 19 residues within 4Å: Chain A: Q.43, L.44, R.58, H.61, D.101, H.104, A.109, H.127, D.205, K.206, Y.209, D.213, R.260, H.264, Y.268, Q.269 Ligands: FE.1, MG.2, MG.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.44, A:Y.268 Hydrogen bonds: A:Q.43, A:L.44, A:L.44, A:R.58, A:R.58, A:D.213, A:Q.269 Water bridges: A:A.109, A:E.128, A:D.203, A:D.205 Salt bridges: A:K.206, A:R.260, A:D.277 T8T.6: 17 residues within 4Å: Chain A: Y.49, V.50, P.52, K.271, V.272, R.345 Chain B: K.10, V.11, I.12, I.30, D.31, Q.36, R.39, F.59 Chain D: K.417 Ligands: MG.14, T8T.23 17 PLIP interactions: 10 interactions with chain B, 2 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: B:I.12 Hydrogen bonds: B:V.11, B:Q.36, B:R.39, A:R.345 Water bridges: B:K.10, B:K.10, B:D.31 Salt bridges: B:K.10, B:K.10, B:D.31, D:K.417, D:K.417, A:K.271, A:K.349, A:K.349 pi-Cation interactions: A:R.345 T8T.8: 20 residues within 4Å: Chain A: D.224, R.227, F.231, R.246, K.248, N.252, K.417 Chain C: V.11, I.12, N.13, H.19 Chain D: V.50, F.51, G.218, I.219, R.266, H.270, K.271 Ligands: MG.7, T8T.24 21 PLIP interactions: 12 interactions with chain A, 6 interactions with chain D, 3 interactions with chain C Hydrogen bonds: A:R.227, A:K.248, A:N.252, D:V.50, C:N.13, C:N.13, C:N.13 Water bridges: A:K.417, A:K.417 Salt bridges: A:D.224, A:R.246, A:K.248, A:K.248, A:K.417, D:H.270, D:K.271, D:K.271 pi-Cation interactions: A:R.227, A:R.227 Hydrophobic interactions: D:V.50, D:F.51 T8T.9: 15 residues within 4Å: Chain A: K.10, V.11, I.12, I.30, D.31, Q.36, R.39, F.59 Chain B: Y.49, V.50, K.271, V.272, R.345 Ligands: MG.4, T8T.10 14 PLIP interactions: 5 interactions with chain B, 8 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:R.345, A:V.11, A:Q.36, A:R.39 Salt bridges: B:K.271, B:K.349, B:K.349, A:K.10, A:K.10, A:D.31 pi-Cation interactions: B:R.345 Hydrophobic interactions: A:I.12 Water bridges: A:V.11, C:K.417 T8T.10: 20 residues within 4Å: Chain A: V.11, I.12, N.13, H.19 Chain B: V.50, F.51, G.218, I.219, R.266, H.270, K.271 Chain C: D.224, R.227, F.231, R.246, K.248, N.252, K.417 Ligands: MG.4, T8T.9 21 PLIP interactions: 6 interactions with chain B, 12 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: B:V.50, B:F.51 Hydrogen bonds: B:V.50, C:R.227, C:N.252, A:N.13, A:N.13, A:H.19 Salt bridges: B:H.270, B:K.271, B:K.271, C:R.246, C:K.248, C:K.248, C:K.417, C:K.417 Water bridges: C:K.417, C:K.417, C:K.417 pi-Cation interactions: C:R.227, C:R.227 T8T.15: 19 residues within 4Å: Chain B: Q.43, L.44, R.58, H.61, D.101, H.104, A.109, H.127, D.205, K.206, Y.209, D.213, R.260, H.264, Y.268, Q.269 Ligands: FE.11, MG.12, MG.13 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.44, B:Y.268 Hydrogen bonds: B:Q.43, B:L.44, B:R.58, B:R.58, B:E.128, B:E.128, B:Y.209, B:D.213, B:Q.269 Water bridges: B:R.260, B:R.260, B:R.260, B:R.260 Salt bridges: B:K.206, B:R.260, B:D.277 T8T.17: 19 residues within 4Å: Chain B: D.224, R.227, F.231, R.246, K.248, N.252, K.417 Chain C: V.50, F.51, I.219, R.266, H.270, K.271 Chain D: V.11, I.12, N.13, H.19 Ligands: MG.16, T8T.22 20 PLIP interactions: 8 interactions with chain C, 10 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: C:V.50, C:F.51 Hydrogen bonds: C:V.50, B:R.227, B:N.252, D:N.13, D:N.13 Water bridges: C:K.271, C:K.271, B:R.246, B:R.246 Salt bridges: C:H.270, C:K.271, C:K.271, B:D.224, B:R.246, B:K.248, B:K.417 pi-Cation interactions: B:R.227, B:R.227 T8T.21: 19 residues within 4Å: Chain C: Q.43, L.44, R.58, H.61, D.101, H.104, A.109, H.127, D.205, K.206, Y.209, D.213, R.260, H.264, Y.268, Q.269 Ligands: FE.18, MG.19, MG.20 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.44, C:Y.268 Hydrogen bonds: C:Q.43, C:L.44, C:L.44, C:R.58, C:R.58, C:D.213, C:Q.269 Water bridges: C:E.128 Salt bridges: C:K.206, C:R.260, C:D.277 T8T.22: 17 residues within 4Å: Chain B: K.417 Chain C: Y.49, V.50, K.271, V.272, R.345, K.349 Chain D: K.10, V.11, I.12, I.30, D.31, Q.36, R.39, F.59 Ligands: MG.16, T8T.17 16 PLIP interactions: 5 interactions with chain C, 9 interactions with chain D, 2 interactions with chain B Hydrogen bonds: C:R.345, D:Q.36, D:R.39 Salt bridges: C:K.271, C:K.349, C:K.349, D:K.10, D:K.10, D:D.31, B:K.417, B:K.417 pi-Cation interactions: C:R.345 Hydrophobic interactions: D:I.12 Water bridges: D:K.10, D:K.10, D:V.11 T8T.23: 21 residues within 4Å: Chain A: V.50, F.51, G.218, I.219, R.266, H.270, K.271, V.272 Chain B: V.11, I.12, N.13, H.19 Chain D: D.224, R.227, F.231, R.246, K.248, N.252, K.417 Ligands: T8T.6, MG.14 20 PLIP interactions: 8 interactions with chain A, 9 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: A:V.50, A:F.51 Hydrogen bonds: A:V.50, D:R.227, D:K.248, D:N.252, B:N.13, B:N.13 Water bridges: A:K.271, A:K.271, B:K.10 Salt bridges: A:H.270, A:K.271, A:K.271, D:D.224, D:R.246, D:K.248, D:K.417 pi-Cation interactions: D:R.227, D:R.227 T8T.24: 16 residues within 4Å: Chain C: K.10, V.11, I.12, I.30, D.31, Q.36, R.39, F.59 Chain D: Y.49, V.50, P.52, K.271, V.272, R.345 Ligands: MG.7, T8T.8 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:I.12 Hydrogen bonds: C:Q.36, C:R.39, D:R.345 Water bridges: C:K.10, C:K.10, C:K.10, C:V.11 Salt bridges: C:K.10, C:K.10, C:D.31, D:K.271, D:K.349 pi-Cation interactions: D:R.345 T8T.28: 19 residues within 4Å: Chain D: Q.43, L.44, R.58, H.61, D.101, H.104, A.109, H.127, D.205, K.206, Y.209, D.213, R.260, H.264, Y.268, Q.269 Ligands: FE.25, MG.26, MG.27 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.44, D:Y.268 Hydrogen bonds: D:Q.43, D:L.44, D:R.58, D:R.58, D:Y.209, D:D.213, D:Q.269 Water bridges: D:E.128, D:D.205, D:R.260, D:R.260 Salt bridges: D:K.206, D:R.260, D:D.277

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morris, E.R. et al., Probing the Catalytic Mechanism and Inhibition of SAMHD1 Using the Differential Properties of R p - and S p -dNTP alpha S Diastereomers. Biochemistry (2021)

Release Date

2021-05-26

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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