SMTL ID : 5yhw.2 (1 other biounit)

Crystal structure of Pig SAMHD1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

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

DGT.1: 16 residues within 4Å: Chain A: Q.46, L.47, R.61, R.103, H.107, H.112, H.130, D.208, K.209, Y.212, D.216, R.263, H.267, Y.271, Q.272 Ligands: MG.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:L.47, A:Y.271 Hydrogen bonds: A:Q.46, A:L.47, A:R.61, A:Y.271, A:Q.272 Water bridges: A:R.103, A:H.112, A:R.263, A:R.263 Salt bridges: A:R.61, A:R.103, A:H.107, A:H.112, A:H.112, A:H.130, A:H.130, A:K.209, A:R.263 pi-Stacking: A:H.112, A:H.267 DGT.3: 15 residues within 4Å: Chain A: Y.52, V.53, V.275, R.348 Chain C: K.13, V.14, I.15, I.33, D.34, Q.39, R.42, F.62 Chain D: K.421 Ligands: DGT.16, MG.17 12 PLIP interactions: 7 interactions with chain C, 3 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: C:I.15 Hydrogen bonds: C:K.13, C:R.42 Salt bridges: C:K.13, C:K.13, C:K.13, C:D.34, A:K.274, A:R.348, D:K.421, D:K.421 pi-Cation interactions: A:R.348 DGT.5: 16 residues within 4Å: Chain A: K.13, V.14, I.15, I.33, D.34, Q.39, R.42, F.62 Chain C: Y.52, V.53, P.55, V.275, R.348, K.352 Ligands: MG.4, DGT.10 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:I.15 Hydrogen bonds: A:Q.39, A:R.42, C:R.348 Water bridges: A:K.13 Salt bridges: A:K.13, A:K.13, A:K.13, A:D.34, C:R.348, C:K.352, C:K.352 pi-Cation interactions: C:R.348 DGT.6: 17 residues within 4Å: Chain A: D.227, R.230, R.249, K.251, N.255 Chain B: V.14, I.15, N.16, H.22 Chain D: V.53, F.54, I.222, R.269, H.273, V.275 Ligands: MG.11, DGT.20 17 PLIP interactions: 5 interactions with chain D, 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: D:V.53, D:F.54 Hydrogen bonds: D:R.269, A:D.227, A:R.230, A:N.255, B:N.16, B:N.16 Salt bridges: D:H.273, D:H.273, A:R.230, A:R.249, A:K.251, A:K.251, A:K.251 pi-Cation interactions: A:R.230, A:R.230 DGT.7: 16 residues within 4Å: Chain B: Q.46, L.47, R.61, R.103, N.104, H.107, H.112, H.130, D.208, K.209, Y.212, D.216, R.263, Y.271, Q.272 Ligands: MG.8 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.47, B:Y.271 Hydrogen bonds: B:Q.46, B:L.47, B:R.61, B:N.104, B:D.208, B:Y.271, B:Q.272 Salt bridges: B:R.61, B:R.103, B:H.107, B:H.130, B:H.130, B:K.209, B:R.263 pi-Stacking: B:H.267 DGT.9: 15 residues within 4Å: Chain B: Y.52, V.53, P.55, V.275, R.348 Chain D: K.13, V.14, I.15, I.33, D.34, Q.39, R.42, F.62 Ligands: DGT.12, MG.15 11 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: D:I.15 Hydrogen bonds: D:Q.39, D:R.42, B:R.348 Salt bridges: D:K.13, D:K.13, D:K.13, D:D.34, C:K.421, B:R.348 pi-Cation interactions: B:R.348 DGT.10: 21 residues within 4Å: Chain A: V.14, I.15, N.16, H.22 Chain B: D.227, R.230, F.234, R.249, K.251, N.255, K.421 Chain C: V.53, F.54, G.221, I.222, R.269, H.273, K.274, V.275 Ligands: MG.4, DGT.5 20 PLIP interactions: 7 interactions with chain C, 11 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: C:V.53, C:F.54 Salt bridges: C:H.273, C:H.273, C:K.274, C:K.274, C:K.274, B:D.227, B:R.230, B:R.249, B:K.251, B:K.251, B:K.251, B:K.421 Hydrogen bonds: B:R.230, B:N.255, A:N.16, A:N.16 pi-Cation interactions: B:R.230, B:R.230 DGT.12: 20 residues within 4Å: Chain B: V.53, F.54, G.221, I.222, R.269, H.273, K.274, V.275 Chain C: D.227, R.230, R.249, K.251, N.255, K.421 Chain D: V.14, I.15, N.16, H.22 Ligands: DGT.9, MG.15 22 PLIP interactions: 11 interactions with chain C, 2 interactions with chain D, 9 interactions with chain B Hydrogen bonds: C:D.227, C:R.230, C:N.255, D:N.16, D:N.16, B:R.269, B:R.269 Salt bridges: C:R.230, C:R.249, C:K.251, C:K.251, C:K.251, C:K.421, B:H.273, B:H.273, B:K.274, B:K.274, B:K.274 pi-Cation interactions: C:R.230, C:R.230 Hydrophobic interactions: B:V.53, B:F.54 DGT.13: 16 residues within 4Å: Chain C: Q.46, L.47, R.61, R.103, N.104, H.107, H.112, H.130, D.208, K.209, Y.212, D.216, R.263, Y.271, Q.272 Ligands: MG.14 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:Y.271 Hydrogen bonds: C:Q.46, C:L.47, C:R.61, C:N.104, C:D.208, C:Y.212, C:Y.271, C:Q.272 Salt bridges: C:R.61, C:R.103, C:R.103, C:H.107, C:H.112, C:H.130, C:H.130, C:K.209, C:K.209, C:R.263 pi-Stacking: C:H.112, C:H.267 DGT.16: 20 residues within 4Å: Chain A: V.53, F.54, G.221, I.222, R.269, H.273, K.274, V.275 Chain C: V.14, I.15, N.16, H.22 Chain D: D.227, R.230, R.249, K.251, N.255, K.421 Ligands: DGT.3, MG.17 18 PLIP interactions: 6 interactions with chain A, 10 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: A:V.53, A:F.54 Salt bridges: A:H.273, A:H.273, A:K.274, A:K.274, D:R.230, D:R.249, D:K.251, D:K.251, D:K.251, D:K.421 Hydrogen bonds: D:R.230, D:N.255, C:N.16, C:N.16 pi-Cation interactions: D:R.230, D:R.230 DGT.18: 15 residues within 4Å: Chain D: Q.46, L.47, R.61, R.103, H.107, H.112, D.208, K.209, Y.212, D.216, R.263, H.267, Y.271, Q.272 Ligands: MG.19 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.47, D:Y.271 Hydrogen bonds: D:Q.46, D:L.47, D:R.61, D:Y.212, D:Q.272 Salt bridges: D:R.61, D:R.103, D:H.107, D:H.112, D:H.130, D:K.209, D:R.263, D:D.280 pi-Stacking: D:H.112 DGT.20: 15 residues within 4Å: Chain B: K.13, V.14, I.15, I.30, I.33, D.34, R.42, F.62 Chain D: Y.52, V.53, P.55, V.275, R.348 Ligands: DGT.6, MG.11 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:I.15 Hydrogen bonds: B:R.42, D:R.348 Salt bridges: B:K.13, B:K.13, B:K.13, B:D.34, D:R.348 pi-Cation interactions: D:R.348

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: R.103, K.209 Ligands: DGT.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: K.13 Ligands: DGT.5, DGT.10 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: R.103, D.206, K.209 Ligands: DGT.7 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain B: K.13 Ligands: DGT.6, DGT.20 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain C: R.103, K.209 Ligands: DGT.13 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain D: K.13 Ligands: DGT.9, DGT.12 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain D: K.421 Ligands: DGT.3, DGT.16 No protein-ligand interaction detected (PLIP) MG.19: 4 residues within 4Å: Chain D: R.103, D.206, K.209 Ligands: DGT.18 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kong, J. et al., Structural characterization and directed modification of Sus scrofa SAMHD1 reveal the mechanism underlying deoxynucleotide regulation. Febs J. (2019)

Release Date

2018-10-17

Peptides

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

C
F

D
G

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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