SMTL ID : 8qxn.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

GTP.1: 16 residues within 4Å: Chain A: K.116, V.117, I.118, V.133, I.136, D.137, R.145, F.165 Chain B: Y.155, V.156, V.378, R.451, K.455 Chain D: K.523 Ligands: DTP.15, MG.16 12 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B, 2 interactions with chain D Hydrogen bonds: A:V.117, A:R.145, B:R.451 Salt bridges: A:K.116, A:K.116, A:D.137, B:K.455, B:K.455, D:K.523, D:K.523 pi-Cation interactions: B:R.451, B:R.451 GTP.6: 15 residues within 4Å: Chain A: Y.155, V.156, V.378, R.451, L.453 Chain B: K.116, V.117, I.118, I.136, D.137, Q.142, R.145, F.165 Ligands: DTP.4, MG.9 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, A:R.451 pi-Cation interactions: A:R.451 GTP.12: 15 residues within 4Å: Chain B: K.523 Chain C: K.116, V.117, I.118, I.136, D.137, Q.142, R.145, F.165 Chain D: Y.155, V.156, V.378, R.451 Ligands: DTP.11, MG.17 11 PLIP interactions: 3 interactions with chain D, 6 interactions with chain C, 2 interactions with chain B Hydrogen bonds: D:R.451, C:V.117, C:Q.142, C:R.145 Salt bridges: D:K.455, C:K.116, C:K.116, C:D.137, B:K.523, B:K.523 pi-Cation interactions: D:R.451 GTP.18: 14 residues within 4Å: Chain C: Y.155, V.156, V.378, R.451 Chain D: K.116, V.117, I.118, V.133, D.137, Q.142, R.145, F.165 Ligands: DTP.5, MG.21 11 PLIP interactions: 4 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:R.451, D:V.117, D:Q.142, D:R.145 Salt bridges: C:R.451, D:K.116, D:K.116, D:K.116, D:D.137 pi-Cation interactions: C:R.451, C:R.451

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

FE.2: 5 residues within 4Å: Chain A: H.167, H.206, D.207, D.311, Y.315 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.7: 5 residues within 4Å: Chain B: H.167, H.206, D.207, D.311 Ligands: DCP.10 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.13: 7 residues within 4Å: Chain C: R.164, H.167, H.206, D.207, D.311, Y.315 Ligands: MG.14 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.167, C:H.206, C:D.207, C:D.311, C:Y.315 FE.19: 5 residues within 4Å: Chain D: H.167, H.206, D.207, D.311 Ligands: DCP.22 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.167, D:H.206, D:D.207, D:D.311

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

MG.3: 3 residues within 4Å: Chain A: D.207, H.210, H.233 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.207, A:H.233 MG.8: 3 residues within 4Å: Chain B: D.207, H.233 Ligands: DCP.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.207, B:H.233 MG.9: 2 residues within 4Å: Ligands: DTP.4, GTP.6 No protein-ligand interaction detected (PLIP) MG.14: 5 residues within 4Å: Chain C: D.207, H.210, H.233, Y.315 Ligands: FE.13 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.207 MG.16: 2 residues within 4Å: Ligands: GTP.1, DTP.15 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Ligands: DTP.11, GTP.12 No protein-ligand interaction detected (PLIP) MG.20: 5 residues within 4Å: Chain D: H.206, D.207, H.210, H.233 Ligands: DCP.22 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.207, D:H.233 MG.21: 2 residues within 4Å: Ligands: DTP.5, GTP.18 No protein-ligand interaction detected (PLIP)

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

DTP.4: 9 residues within 4Å: Chain A: V.156, F.157, R.372, H.376 Chain B: N.119, H.125 Chain C: R.333 Ligands: GTP.6, MG.9 10 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: C:R.333, B:N.119, B:N.119 Salt bridges: C:K.354, C:K.354, C:K.354, A:H.376, A:H.376 pi-Cation interactions: C:R.333 Hydrophobic interactions: A:F.157 DTP.5: 10 residues within 4Å: Chain A: R.333, K.354 Chain C: V.156, F.157, I.325, R.372, H.376 Chain D: N.119 Ligands: GTP.18, MG.21 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:R.333, A:R.333, A:N.358, C:R.372, C:R.372 Salt bridges: A:K.354, A:K.354, A:K.354, C:H.376, C:H.376 pi-Cation interactions: A:R.333, A:R.333 Hydrophobic interactions: C:F.157 DTP.11: 12 residues within 4Å: Chain B: R.333, R.352, K.354, K.523 Chain C: V.117, N.119 Chain D: V.156, F.157, R.372, H.376 Ligands: GTP.12, MG.17 13 PLIP interactions: 7 interactions with chain B, 5 interactions with chain D, 1 interactions with chain C 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 Hydrogen bonds: D:R.372, C:N.119 DTP.15: 13 residues within 4Å: Chain A: V.117, N.119, H.125 Chain B: V.156, F.157, R.372, H.376 Chain D: R.333, R.352, K.354, K.523 Ligands: GTP.1, MG.16 15 PLIP interactions: 4 interactions with chain B, 9 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: B:V.156 Hydrogen bonds: B:R.372, D:R.333, A:N.119, A:N.119 Salt bridges: B:H.376, B:H.376, D:R.333, D:R.352, D:K.354, D:K.354, D:K.354, D:K.523 pi-Cation interactions: D:R.333, D:R.333

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

DCP.10: 15 residues within 4Å: Chain B: 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.7, MG.8 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.150, B:Y.374, B:Y.374 Hydrogen bonds: B:Q.149, B:D.311, B:Y.315, B:D.319, B:R.366, B:Y.374, B:Q.375 Salt bridges: B:R.164, B:H.215, B:H.215 DCP.22: 15 residues within 4Å: Chain D: Q.149, R.164, H.167, D.207, H.210, H.215, D.311, K.312, Y.315, D.319, H.370, Y.374, Q.375 Ligands: FE.19, MG.20 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:Y.374 Hydrogen bonds: D:R.164, D:D.319, D:Q.375 Salt bridges: D:R.164, D:H.167, D:H.215, D:K.312 pi-Stacking: D:H.215, D:Y.374

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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