SMTL ID : 8qxl.1

Cryo-EM structure of tetrameric human SAMHD1 State II - Hemi-relaxed

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

GTP.1: 17 residues within 4Å: Chain A: K.116, V.117, I.118, V.133, I.136, D.137, Q.142, R.145, F.165 Chain B: Y.155, V.156, V.378, R.451, K.455 Chain D: K.523 Ligands: MG.4, DTP.22 14 PLIP interactions: 7 interactions with chain A, 6 interactions with chain B, 1 interactions with chain D Hydrogen bonds: A:V.117, A:Q.142, A:R.145, B:R.451 Salt bridges: A:K.116, A:K.116, A:K.116, A:D.137, B:R.451, B:K.455, B:K.455, D:K.523 pi-Cation interactions: B:R.451, B:R.451 GTP.7: 14 residues within 4Å: Chain A: Y.155, V.156, V.378, R.451, L.453 Chain B: K.116, V.117, I.118, D.137, Q.142, R.145, F.165 Ligands: DTP.8, MG.13 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:R.451, B:V.117, B:Q.142, B:R.145 Salt bridges: A:R.451, A:K.455, B:K.116, B:K.116, B:K.116, B:D.137 pi-Cation interactions: A:R.451 GTP.16: 15 residues within 4Å: Chain B: K.523 Chain C: K.116, V.117, I.118, D.137, Q.142, R.145, F.165 Chain D: Y.155, V.156, V.378, R.451, K.455 Ligands: DTP.15, MG.19 12 PLIP interactions: 1 interactions with chain B, 6 interactions with chain C, 5 interactions with chain D Salt bridges: B:K.523, C:K.116, C:K.116, C:D.137, D:R.451, 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.23: 12 residues within 4Å: Chain C: Y.155, V.156, R.451 Chain D: K.116, V.117, I.118, D.137, Q.142, R.145, F.165 Ligands: DTP.9, MG.27 12 PLIP interactions: 5 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, C:K.455, 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:Y.315 FE.10: 6 residues within 4Å: Chain B: R.164, H.167, H.206, D.207, D.311 Ligands: DCP.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.167, B:H.206, B:D.207, B:D.311 FE.17: 4 residues within 4Å: Chain C: H.167, H.206, D.207, Y.315 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.206, C:D.207 FE.24: 4 residues within 4Å: Chain D: H.167, H.206, D.207, D.311 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.167, D:H.206, D:D.207, D:D.311

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

MG.3: 4 residues within 4Å: Chain A: D.207, H.233, E.234 Ligands: 3PO.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.207 MG.4: 3 residues within 4Å: Chain A: K.116 Ligands: GTP.1, DTP.22 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain B: D.207, H.233 Ligands: DCP.14 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.207 MG.12: 1 residues within 4Å: Ligands: DCP.14 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain B: K.116 Ligands: GTP.7, DTP.8 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain C: D.207, H.233 Ligands: 3PO.21 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain C: K.116 Ligands: DTP.15, GTP.16 No protein-ligand interaction detected (PLIP) MG.25: 4 residues within 4Å: Chain D: D.207, H.210, H.233 Ligands: DCP.28 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.233 MG.26: 1 residues within 4Å: Ligands: DCP.28 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain D: K.116 Ligands: DTP.9, GTP.23 No protein-ligand interaction detected (PLIP)

2 x DCZ: 2'-DEOXYCYTIDINE(Non-covalent)

DCZ.5: 9 residues within 4Å: Chain A: Q.149, L.150, R.164, H.215, Y.315, D.319, Y.374, Q.375 Ligands: 3PO.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.150, A:Y.374 Hydrogen bonds: A:Y.315, A:Y.374, A:Q.375 DCZ.20: 4 residues within 4Å: Chain C: H.215, Y.315, Y.374 Ligands: 3PO.21 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.374, C:Y.374

2 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.6: 9 residues within 4Å: Chain A: H.215, H.233, D.311, K.312, Y.315, R.366, H.370 Ligands: MG.3, DCZ.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.311 Salt bridges: A:H.215, A:H.233, A:K.312, A:K.312, A:R.366, A:H.370 3PO.21: 7 residues within 4Å: Chain C: H.233, E.234, D.309, K.312, Y.315 Ligands: MG.18, DCZ.20 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.234 Salt bridges: C:K.312, C:K.312, C:K.312

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

DTP.8: 13 residues within 4Å: Chain A: V.156, F.157, I.325, R.372, H.376 Chain B: V.117, N.119 Chain C: R.333, R.352, K.354, K.523 Ligands: GTP.7, MG.13 13 PLIP interactions: 7 interactions with chain C, 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:R.333, A:R.372, B:N.119 Salt bridges: C:R.333, C:R.352, C:K.354, C:K.523, A:H.376, A:H.376 pi-Cation interactions: C:R.333, C:R.333 Hydrophobic interactions: A:V.156, A:F.157 DTP.9: 15 residues within 4Å: Chain A: R.333, R.352, K.354, N.358, K.523 Chain C: V.156, F.157, R.372, H.376 Chain D: V.117, I.118, N.119, H.125 Ligands: GTP.23, MG.27 12 PLIP interactions: 9 interactions with chain A, 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: A:R.333, A:N.358, D:N.119 Salt bridges: A:R.333, A:R.352, A:K.354, A:K.354, A:K.523, C:H.376 pi-Cation interactions: A:R.333, A:R.333 Hydrophobic interactions: C:F.157 DTP.15: 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.16, MG.19 14 PLIP interactions: 8 interactions with chain B, 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: B:R.333, C:N.119, C:N.119 Salt bridges: B:R.333, B:R.352, B:K.354, B:K.354, B:K.523, D:H.376, D:H.376 pi-Cation interactions: B:R.333, B:R.333 Hydrophobic interactions: D:V.156, D:F.157 DTP.22: 17 residues within 4Å: Chain A: V.117, I.118, N.119, H.125 Chain B: V.156, F.157, I.325, R.372, H.376, K.377, V.378 Chain D: R.333, R.352, K.354, K.523 Ligands: GTP.1, MG.4 18 PLIP interactions: 9 interactions with chain D, 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: D:R.333, B:R.372, B: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, B:H.376, B:H.376, B:K.377, B:K.377 pi-Cation interactions: D:R.333, D:R.333 Hydrophobic interactions: B:V.156, B:F.157

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

DCP.14: 15 residues within 4Å: Chain B: Q.149, L.150, R.164, H.210, H.215, D.311, K.312, Y.315, D.319, R.366, Y.374, Q.375 Ligands: FE.10, MG.11, MG.12 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.150, B:Y.374 Hydrogen bonds: B:Q.149, B:Y.315, B:Y.315, B:D.319, B:Q.375 Salt bridges: B:R.164, B:H.215, B:H.215, B:K.312, B:R.366 DCP.28: 12 residues within 4Å: Chain D: Q.149, L.150, H.215, H.233, D.311, K.312, Y.315, D.319, R.366, Y.374 Ligands: MG.25, MG.26 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:L.150, D:Y.374, D:Y.374 Hydrogen bonds: D:Q.149, D:D.311, D:Y.315, D:D.319, D:Y.374, D:Q.375 Salt bridges: D:H.215, D:K.312, D:R.366

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

Related Entries With Identical Sequence