SMTL ID : 8qxk.1

Cryo-EM structure of tetrameric human SAMHD1 State I - Tense

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

GTP.1: 15 residues within 4Å: Chain A: K.116, V.117, I.118, D.137, Q.142, R.145, F.165 Chain C: Y.155, V.156, V.378, R.451, K.455 Chain D: K.523 Ligands: MG.5, DTP.22 13 PLIP interactions: 7 interactions with chain A, 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: A:V.117, A:Q.142, A:R.145, C:R.451 Salt bridges: A:K.116, A:K.116, A:K.116, A:D.137, C:R.451, C:K.455, C:K.455, D:K.523 pi-Cation interactions: C:R.451 GTP.8: 15 residues within 4Å: Chain B: K.116, V.117, I.118, D.137, Q.142, R.145, F.165 Chain C: K.523 Chain D: Y.155, V.156, V.378, R.451, K.455 Ligands: MG.12, DTP.15 13 PLIP interactions: 7 interactions with chain B, 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: B:V.117, B:Q.142, B:R.145, D:R.451 Salt bridges: B:K.116, B:K.116, B:K.116, B:D.137, D:R.451, D:K.455, D:K.455, C:K.523 pi-Cation interactions: D:R.451 GTP.16: 15 residues within 4Å: Chain A: Y.155, V.156, V.378, R.451, K.455 Chain B: K.523 Chain C: K.116, V.117, I.118, D.137, Q.142, R.145, F.165 Ligands: DTP.14, MG.20 13 PLIP interactions: 1 interactions with chain B, 7 interactions with chain C, 5 interactions with chain A Salt bridges: B:K.523, C:K.116, C:K.116, C:K.116, C:D.137, A:R.451, A:K.455, A:K.455 Hydrogen bonds: C:V.117, C:Q.142, C:R.145, A:R.451 pi-Cation interactions: A:R.451 GTP.23: 15 residues within 4Å: Chain A: K.523 Chain B: Y.155, V.156, V.378, R.451, K.455 Chain D: K.116, V.117, I.118, D.137, Q.142, R.145, F.165 Ligands: DTP.7, MG.27 13 PLIP interactions: 5 interactions with chain B, 7 interactions with chain D, 1 interactions with chain A Hydrogen bonds: B:R.451, D:V.117, D:Q.142, D:R.145 Salt bridges: B:R.451, B:K.455, B:K.455, D:K.116, D:K.116, D:K.116, D:D.137, A:K.523 pi-Cation interactions: B:R.451

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

FE.2: 6 residues within 4Å: Chain A: R.164, H.167, H.206, D.207, D.311 Ligands: DCP.6 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.167, A:H.206, A:D.207, A:D.311, A:D.311 FE.9: 6 residues within 4Å: Chain B: R.164, H.167, H.206, D.207, D.311 Ligands: DCP.13 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.167, B:H.206, B:D.207, B:D.311, B:D.311 FE.17: 6 residues within 4Å: Chain C: R.164, H.167, H.206, D.207, D.311 Ligands: DCP.21 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.167, C:H.206, C:D.207, C:D.311, C:D.311 FE.24: 6 residues within 4Å: Chain D: R.164, H.167, H.206, D.207, D.311 Ligands: DCP.28 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.167, D:H.206, D:D.207, D:D.311, D:D.311

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

MG.3: 4 residues within 4Å: Chain A: D.207, H.233, E.234 Ligands: DCP.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.207, A:H.233 MG.4: 3 residues within 4Å: Chain A: S.302, D.309 Ligands: DCP.6 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: K.116 Ligands: GTP.1, DTP.22 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain B: D.207, H.233, E.234 Ligands: DCP.13 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.207, B:H.233 MG.11: 3 residues within 4Å: Chain B: S.302, D.309 Ligands: DCP.13 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Ligands: GTP.8, DTP.15 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain C: D.207, H.233, E.234 Ligands: DCP.21 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.207, C:H.233 MG.19: 3 residues within 4Å: Chain C: S.302, D.309 Ligands: DCP.21 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Ligands: DTP.14, GTP.16 No protein-ligand interaction detected (PLIP) MG.25: 4 residues within 4Å: Chain D: D.207, H.233, E.234 Ligands: DCP.28 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.207, D:H.233 MG.26: 3 residues within 4Å: Chain D: S.302, D.309 Ligands: DCP.28 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain D: K.116 Ligands: DTP.7, GTP.23 No protein-ligand interaction detected (PLIP)

4 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.6: 17 residues within 4Å: Chain A: Q.149, L.150, R.164, D.207, H.210, H.215, H.233, D.311, K.312, Y.315, D.319, R.366, Y.374, Q.375 Ligands: FE.2, MG.3, MG.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.150, A:Y.374 Hydrogen bonds: A:Q.149, A:D.207, A:Y.315, A:D.319, A:Q.375 Salt bridges: A:R.164, A:H.210, A:H.215, A:H.215, A:H.233, A:K.312, A:R.366 DCP.13: 17 residues within 4Å: Chain B: Q.149, L.150, R.164, D.207, H.210, H.215, H.233, D.311, K.312, Y.315, D.319, R.366, Y.374, Q.375 Ligands: FE.9, MG.10, MG.11 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.150, B:Y.374 Hydrogen bonds: B:Q.149, B:Y.315, B:D.319, B:Q.375 Salt bridges: B:R.164, B:H.210, B:H.215, B:H.215, B:H.233, B:K.312, B:R.366 DCP.21: 17 residues within 4Å: Chain C: Q.149, L.150, R.164, D.207, H.210, H.215, H.233, D.311, K.312, Y.315, D.319, R.366, Y.374, Q.375 Ligands: FE.17, MG.18, MG.19 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.150, C:Y.374 Hydrogen bonds: C:Q.149, C:Y.315, C:Y.374, C:Q.375 Salt bridges: C:R.164, C:H.210, C:H.215, C:H.215, C:H.233, C:K.312, C:R.366 DCP.28: 16 residues within 4Å: Chain D: Q.149, L.150, R.164, D.207, H.210, H.215, D.311, K.312, Y.315, D.319, R.366, Y.374, Q.375 Ligands: FE.24, MG.25, MG.26 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:L.150, D:Y.374 Hydrogen bonds: D:Q.149, D:D.207, D:Y.315, D:Y.374, D:Q.375 Salt bridges: D:R.164, D:H.210, D:H.215, D:H.215, D:H.233, D:K.312, D:R.366 pi-Stacking: D:H.215

4 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.7: 13 residues within 4Å: Chain A: R.333, R.352, K.354, N.358, K.523 Chain B: V.156, F.157, R.372, H.376 Chain D: V.117, N.119 Ligands: GTP.23, MG.27 16 PLIP interactions: 10 interactions with chain A, 5 interactions with chain B, 1 interactions with chain D Hydrogen bonds: A:R.333, A:N.358, A:N.358, B:R.372, D:N.119 Salt bridges: A:R.333, A:R.352, A:K.354, A:K.354, A:K.523, B:H.376, B:H.376 pi-Cation interactions: A:R.333, A:R.333 Hydrophobic interactions: B:V.156, B:F.157 DTP.14: 13 residues within 4Å: Chain A: V.156, F.157, R.372, H.376 Chain B: R.333, R.352, K.354, N.358, K.523 Chain C: V.117, N.119 Ligands: GTP.16, MG.20 17 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:R.333, B:N.358, B:N.358, A:R.372, C:N.119 Salt bridges: B:R.333, B:R.352, B:K.354, B:K.354, B:K.354, B:K.523, A:H.376, A:H.376 pi-Cation interactions: B:R.333, B:R.333 Hydrophobic interactions: A:V.156, A:F.157 DTP.15: 13 residues within 4Å: Chain B: V.117, N.119 Chain C: R.333, R.352, K.354, N.358, K.523 Chain D: V.156, F.157, R.372, H.376 Ligands: GTP.8, MG.12 17 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B, 5 interactions with chain D Hydrogen bonds: C:R.333, C:N.358, C:N.358, B:N.119, D:R.372 Salt bridges: C:R.333, C:R.352, C:K.354, C:K.354, C:K.354, C:K.523, D:H.376, D:H.376 pi-Cation interactions: C:R.333, C:R.333 Hydrophobic interactions: D:V.156, D:F.157 DTP.22: 13 residues within 4Å: Chain A: V.117, N.119 Chain C: V.156, F.157, R.372, H.376 Chain D: R.333, R.352, K.354, N.358, K.523 Ligands: GTP.1, MG.5 17 PLIP interactions: 11 interactions with chain D, 5 interactions with chain C, 1 interactions with chain A Hydrogen bonds: D:R.333, D:N.358, D:N.358, C:R.372, A:N.119 Salt bridges: D:R.333, D:R.352, D:K.354, D:K.354, D:K.354, D:K.523, C:H.376, C:H.376 pi-Cation interactions: D:R.333, D:R.333 Hydrophobic interactions: C:V.156, C:F.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Acton, O.J. et al., Platform-directed allostery and quaternary structure dynamics of SAMHD1 catalysis. Nat Commun (2024)

Release Date

2024-05-15

Peptides

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
D

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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