SMTL ID : 8qxo.1

Cryo-EM structure of tetrameric human SAMHD1 State V - Depleted relaxed

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, I.136, D.137, Q.142, R.145, F.165 Chain B: Y.155, V.156, V.378, R.451, K.455 Ligands: MG.3, DTP.4 10 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D, 6 interactions with chain A Hydrogen bonds: B:R.451, A:V.117, A:Q.142, A:R.145 Salt bridges: B:K.455, D:K.523, A:K.116, A:K.116, A:D.137 pi-Cation interactions: B:R.451 GTP.5: 13 residues within 4Å: Chain A: Y.155, V.156, V.378, R.451 Chain B: K.116, V.117, I.118, V.133, I.136, D.137, Q.142, R.145, F.165 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:V.117, B:Q.142, B:R.145, A:R.451 Salt bridges: B:K.116, B:K.116, B:K.116, B:D.137 pi-Cation interactions: A:R.451, A:R.451 GTP.11: 16 residues within 4Å: Chain B: K.523 Chain C: K.116, V.117, I.118, V.133, I.136, D.137, Q.142, F.165 Chain D: Y.155, V.156, V.378, R.451, K.455 Ligands: DTP.8, MG.10 12 PLIP interactions: 1 interactions with chain B, 7 interactions with chain C, 4 interactions with chain D Salt bridges: B:K.523, C:K.116, C:K.116, C:K.116, C:D.137, D:K.455, D:K.455 Hydrogen bonds: C:V.117, C:Q.142, C:R.145, D:R.451 pi-Cation interactions: D:R.451 GTP.12: 10 residues within 4Å: Chain C: Y.155, V.156, V.378, R.451, L.453 Chain D: K.116, V.117, I.118, R.145, F.165 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:K.116, D:K.116, D:V.117, D:R.145, C:R.451 Salt bridges: D:K.116, D:K.116, D:K.116, C:R.451 pi-Cation interactions: C:R.451

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

FE.2: 4 residues within 4Å: Chain A: H.167, H.206, D.207, D.311 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.167, A:H.206, A:D.207, A:D.311 FE.6: 6 residues within 4Å: Chain B: R.164, H.167, H.206, D.207, D.311 Ligands: DCP.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.167, B:H.206, B:D.311, B:D.311 FE.9: 4 residues within 4Å: Chain C: H.167, H.206, D.207, D.311 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.167, C:H.206, C:D.207, C:D.311 FE.13: 6 residues within 4Å: Chain D: R.164, H.167, H.206, D.207, D.311 Ligands: DCP.14 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.167, D:H.206, D:D.207, D:D.311

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: K.116 Ligands: GTP.1, DTP.4 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain C: K.116 Ligands: DTP.8, GTP.11 No protein-ligand interaction detected (PLIP)

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

DTP.4: 15 residues within 4Å: Chain A: V.117, I.118, N.119, H.125 Chain B: V.156, F.157, R.372, H.376, K.377, V.378 Chain D: R.333, F.337, K.523 Ligands: GTP.1, MG.3 14 PLIP interactions: 5 interactions with chain B, 6 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: B:F.157 Salt bridges: B:H.376, B:H.376, B:K.377, D:R.333, D:K.354, D:K.523, A:K.116 pi-Stacking: B:F.157 Hydrogen bonds: D:R.333, A:N.119, A:N.119 pi-Cation interactions: D:R.333, D:R.333 DTP.8: 15 residues within 4Å: Chain B: R.333, F.337, R.352, K.354, N.358, K.523 Chain C: V.117, N.119 Chain D: V.156, F.157, I.325, R.372, H.376 Ligands: MG.10, GTP.11 15 PLIP interactions: 10 interactions with chain B, 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: B:R.333, B:N.358, B:N.358, C:N.119 Salt bridges: B:R.333, B:R.352, B:K.354, B:K.354, B:K.354, B:K.523, D:H.376, D:H.376 pi-Cation interactions: B:R.333 Hydrophobic interactions: D:V.156, D:F.157

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

DCP.7: 10 residues within 4Å: Chain B: L.150, R.164, H.206, H.210, H.215, H.233, D.311, Y.315, Y.374 Ligands: FE.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.150, B:Y.374 Hydrogen bonds: B:R.164, B:H.206, B:Y.374 Salt bridges: B:H.206, B:H.210, B:H.215, B:H.233 DCP.14: 13 residues within 4Å: Chain D: Q.149, L.150, R.164, D.207, H.215, D.311, Y.315, D.319, R.366, H.370, Y.374, Q.375 Ligands: FE.13 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:Y.374 Hydrogen bonds: D:R.164, D:D.311, D:Y.315, D:D.319, D:R.366, D:Q.375 Salt bridges: D:R.164 pi-Stacking: D:Y.374 pi-Cation interactions: D:H.215

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
B

C
C

D
D

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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