SMTL ID : 8qxj.1

Cryo-EM structure of tetrameric human SAMHD1 with dApNHpp

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

8 x DZ4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine(Non-covalent)

DZ4.1: 19 residues within 4Å: Chain A: Q.149, L.150, R.164, H.167, H.206, 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 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.374 Hydrogen bonds: A:Q.149, A:R.164, A:R.164, A:H.215, A:Y.374, A:Q.375 Salt bridges: A:K.312, A:R.366 pi-Stacking: A:H.215 DZ4.7: 14 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 Ligands: GTP.21, MG.28 15 PLIP interactions: 9 interactions with chain A, 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: A:R.333, A:R.333, A:K.354, A:N.358, C:V.156, C:R.372, D:N.119, D:N.119 Salt bridges: A:R.352, A:K.354, A:K.523 pi-Cation interactions: A:R.333, A:R.333 Hydrophobic interactions: C:V.156, C:F.157 DZ4.9: 19 residues within 4Å: Chain B: Q.149, L.150, R.164, H.167, H.206, D.207, H.210, H.215, H.233, D.311, K.312, Y.315, D.319, R.366, Y.374, Q.375 Ligands: FE.10, MG.11, MG.12 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.374 Hydrogen bonds: B:Q.149, B:R.164, B:R.164, B:Y.315, B:Y.374, B:Q.375 Salt bridges: B:K.312, B:R.366 pi-Stacking: B:H.215 DZ4.14: 15 residues within 4Å: Chain B: R.333, R.352, K.354, N.358, K.523 Chain C: V.117, I.118, N.119 Chain D: V.156, F.157, I.325, R.372, H.376 Ligands: MG.20, GTP.23 15 PLIP interactions: 10 interactions with chain B, 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: B:R.333, B:R.333, B:K.354, B:N.358, B:N.358, D:V.156, C:N.119, C:N.119 Salt bridges: B:R.352, B:K.354, B:K.523 pi-Cation interactions: B:R.333, B:R.333 Hydrophobic interactions: D:V.156, D:F.157 DZ4.15: 14 residues within 4Å: Chain A: V.156, F.157, R.372, H.376 Chain B: V.117, N.119, H.125 Chain C: R.333, R.352, K.354, N.358, K.523 Ligands: GTP.6, MG.13 15 PLIP interactions: 9 interactions with chain C, 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: C:R.333, C:R.333, C:K.354, C:N.358, A:V.156, A:R.372, B:N.119, B:N.119 Salt bridges: C:R.352, C:K.354, C:K.523 pi-Cation interactions: C:R.333, C:R.333 Hydrophobic interactions: A:V.156, A:F.157 DZ4.16: 19 residues within 4Å: Chain C: Q.149, L.150, R.164, H.167, H.206, 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 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Y.374 Hydrogen bonds: C:Q.149, C:R.164, C:R.164, C:H.215, C:Y.315, C:Y.374, C:Q.375 Salt bridges: C:K.312, C:R.366 pi-Stacking: C:H.215 DZ4.22: 14 residues within 4Å: Chain A: V.117, N.119 Chain B: V.156, F.157, I.325, R.372, H.376 Chain D: R.333, R.352, K.354, N.358, K.523 Ligands: MG.5, GTP.8 15 PLIP interactions: 10 interactions with chain D, 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: D:R.333, D:R.333, D:K.354, D:N.358, D:N.358, B:V.156, A:N.119, A:N.119 Salt bridges: D:R.352, D:K.354, D:K.523 pi-Cation interactions: D:R.333, D:R.333 Hydrophobic interactions: B:V.156, B:F.157 DZ4.24: 19 residues within 4Å: Chain D: Q.149, L.150, R.164, H.167, H.206, D.207, H.210, H.215, H.233, D.311, K.312, Y.315, D.319, R.366, Y.374, Q.375 Ligands: FE.25, MG.26, MG.27 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:Y.374 Hydrogen bonds: D:Q.149, D:R.164, D:R.164, D:H.215, D:Y.374, D:Q.375 Salt bridges: D:K.312, D:R.366 pi-Stacking: D:H.215

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

FE.2: 6 residues within 4Å: Chain A: H.167, H.206, D.207, D.311 Ligands: DZ4.1, MG.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.167, A:H.206, A:D.207, A:D.311 FE.10: 5 residues within 4Å: Chain B: H.167, H.206, D.207, D.311 Ligands: DZ4.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.167, B:H.206, B:D.207, B:D.311 FE.17: 5 residues within 4Å: Chain C: H.167, H.206, D.207, D.311 Ligands: DZ4.16 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.167, C:H.206, C:D.207, C:D.311 FE.25: 5 residues within 4Å: Chain D: H.167, H.206, D.207, D.311 Ligands: DZ4.24 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.167, D:H.206, D:D.207, D:D.311

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

MG.3: 5 residues within 4Å: Chain A: H.206, D.207, H.233 Ligands: DZ4.1, FE.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.207, A:H.233 MG.4: 1 residues within 4Å: Ligands: DZ4.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: K.116 Ligands: GTP.8, DZ4.22 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain B: H.206, D.207, H.233 Ligands: DZ4.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.207, B:H.233 MG.12: 1 residues within 4Å: Ligands: DZ4.9 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain B: K.116 Ligands: GTP.6, DZ4.15 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain C: H.206, D.207, H.233 Ligands: DZ4.16 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.207, C:H.233 MG.19: 1 residues within 4Å: Ligands: DZ4.16 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain C: K.116 Ligands: DZ4.14, GTP.23 No protein-ligand interaction detected (PLIP) MG.26: 4 residues within 4Å: Chain D: H.206, D.207, H.233 Ligands: DZ4.24 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.207, D:H.233 MG.27: 1 residues within 4Å: Ligands: DZ4.24 No protein-ligand interaction detected (PLIP) MG.28: 3 residues within 4Å: Chain D: K.116 Ligands: DZ4.7, GTP.21 No protein-ligand interaction detected (PLIP)

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

GTP.6: 15 residues within 4Å: Chain A: Y.155, V.156, V.378, R.451, K.455 Chain B: K.116, V.117, I.118, D.137, Q.142, R.145, F.165 Chain C: K.523 Ligands: MG.13, DZ4.15 15 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C, 5 interactions with chain A Hydrogen bonds: B:V.117, B:Q.142, B:R.145, A:R.451 Water bridges: B:V.117 Salt bridges: B:K.116, B:K.116, B:K.116, B:D.137, C:K.523, C:K.523, A:R.451, A:K.455, A:K.455 pi-Cation interactions: A:R.451 GTP.8: 15 residues within 4Å: Chain A: K.116, V.117, I.118, 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.5, DZ4.22 14 PLIP interactions: 5 interactions with chain B, 8 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:R.451, A:V.117, A:Q.142, A:R.145 Salt bridges: B:R.451, B:K.455, B:K.455, A:K.116, A:K.116, A:K.116, A:D.137, D:K.523 pi-Cation interactions: B:R.451 Water bridges: A:V.117 GTP.21: 15 residues within 4Å: Chain A: K.523 Chain C: 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: DZ4.7, MG.28 14 PLIP interactions: 8 interactions with chain D, 5 interactions with chain C, 1 interactions with chain A Hydrogen bonds: D:V.117, D:Q.142, D:R.145, C:R.451 Water bridges: D:V.117 Salt bridges: D:K.116, D:K.116, D:K.116, D:D.137, C:R.451, C:K.455, C:K.455, A:K.523 pi-Cation interactions: C:R.451 GTP.23: 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: DZ4.14, MG.20 14 PLIP interactions: 5 interactions with chain D, 8 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:R.451, C:V.117, C:Q.142, C:R.145 Salt bridges: D:R.451, D:K.455, D:K.455, C:K.116, C:K.116, C:K.116, C:D.137, B:K.523 pi-Cation interactions: D:R.451 Water bridges: C:V.117

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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