- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-tetramer
- Ligands
- 4 x FE: FE (III) ION(Non-covalent)
- 10 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.2: 2 residues within 4Å:- Chain A: D.207, H.233
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:D.207, A:H.233
MG.3: 3 residues within 4Å:- Chain A: K.116
- Ligands: GTP.5, DTP.19
No protein-ligand interaction detected (PLIP)MG.8: 4 residues within 4Å:- Chain B: D.207, H.233, E.234
- Ligands: DCP.11
No protein-ligand interaction detected (PLIP)MG.9: 1 residues within 4Å:- Ligands: DCP.11
No protein-ligand interaction detected (PLIP)MG.10: 3 residues within 4Å:- Chain B: K.116
- Ligands: GTP.6, DTP.13
No protein-ligand interaction detected (PLIP)MG.16: 3 residues within 4Å:- Chain C: D.207, H.233, E.234
2 PLIP interactions:2 interactions with chain C- Metal complexes: C:D.207, C:H.233
MG.17: 3 residues within 4Å:- Chain C: K.116
- Ligands: DTP.12, GTP.14
No protein-ligand interaction detected (PLIP)MG.18: 2 residues within 4Å:- Ligands: DTP.4, GTP.20
No protein-ligand interaction detected (PLIP)MG.22: 4 residues within 4Å:- Chain D: D.207, H.233, E.234
- Ligands: DCP.24
2 PLIP interactions:2 interactions with chain D- Metal complexes: D:D.207, D:H.233
MG.23: 1 residues within 4Å:- Ligands: DCP.24
No protein-ligand interaction detected (PLIP)- 4 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)
DTP.4: 13 residues within 4Å:- Chain A: R.333, R.352, K.354, K.523
- Chain C: V.156, F.157, R.372, H.376
- Chain D: V.117, N.119, H.125
- Ligands: MG.18, GTP.20
15 PLIP interactions:5 interactions with chain C, 9 interactions with chain A, 1 interactions with chain D- Hydrophobic interactions: C:V.156, C:F.157
- Hydrogen bonds: C:R.372, A:R.333, D:N.119
- Salt bridges: C:H.376, C:H.376, A:R.333, A:R.352, A:K.354, A:K.354, A:K.354, A:K.523
- pi-Cation interactions: A:R.333, A:R.333
DTP.12: 13 residues within 4Å:- Chain B: R.333, R.352, K.354, N.358, K.523
- Chain C: V.117, N.119
- Chain D: V.156, F.157, R.372, H.376
- Ligands: GTP.14, MG.17
17 PLIP interactions:11 interactions with chain B, 5 interactions with chain D, 1 interactions with chain C- Hydrogen bonds: B:R.333, B:N.358, B:N.358, D: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, D:H.376, D:H.376
- pi-Cation interactions: B:R.333, B:R.333
- Hydrophobic interactions: D:V.156, D:F.157
DTP.13: 13 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, K.523
- Ligands: GTP.6, MG.10
16 PLIP interactions:6 interactions with chain A, 9 interactions with chain C, 1 interactions with chain B- Hydrophobic interactions: A:V.156, A:F.157
- Hydrogen bonds: A:R.372, A:R.372, C:R.333, C:R.333, B:N.119
- Salt bridges: A:H.376, A:H.376, C:R.352, C:K.354, C:K.354, C:K.354, C:K.523
- pi-Cation interactions: C:R.333, C:R.333
DTP.19: 13 residues within 4Å:- Chain A: V.117, N.119
- Chain B: V.156, F.157, R.372, H.376
- Chain D: R.333, R.352, K.354, N.358, K.523
- Ligands: MG.3, GTP.5
18 PLIP interactions:11 interactions with chain D, 5 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: D:R.333, D:N.358, D:N.358, B:R.372, A:N.119, 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
- pi-Cation interactions: D:R.333, D:R.333
- Hydrophobic interactions: B:V.156, B:F.157
- 4 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)
GTP.5: 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.3, DTP.19
12 PLIP interactions:4 interactions with chain B, 1 interactions with chain D, 7 interactions with chain A- Hydrogen bonds: B:R.451, A:V.117, A:Q.142, A:R.145
- Salt bridges: B:R.451, B:K.455, D:K.523, A:K.116, A:K.116, A:K.116, A:D.137
- pi-Cation interactions: 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: MG.10, DTP.13
11 PLIP interactions:8 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:V.117, 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.14: 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.12, MG.17
12 PLIP interactions:7 interactions with chain C, 4 interactions with chain D, 1 interactions with chain B- Hydrogen bonds: C:V.117, C:Q.142, C:R.145, D:R.451
- Salt bridges: C:K.116, C:K.116, C:K.116, C:D.137, D:R.451, D:K.455, B:K.523
- pi-Cation interactions: D:R.451
GTP.20: 15 residues within 4Å:- Chain C: Y.155, V.156, V.378, R.451, L.453
- Chain D: K.116, V.117, I.118, I.136, D.137, Q.142, R.145, F.165
- Ligands: DTP.4, MG.18
10 PLIP interactions:7 interactions with chain D, 3 interactions with chain C- Hydrogen bonds: D:V.117, D:Q.142, D:R.145, C:R.451
- Salt bridges: D:K.116, D:K.116, D:K.116, D:D.137, C:R.451
- pi-Cation interactions: C:R.451
- 2 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)
DCP.11: 13 residues within 4Å:- Chain B: L.150, R.164, H.210, H.215, D.311, K.312, Y.315, D.319, R.366, Y.374
- Ligands: FE.7, MG.8, MG.9
11 PLIP interactions:11 interactions with chain B- Hydrophobic interactions: B:L.150, B:Y.374
- Hydrogen bonds: B:Q.149, B:H.210, B:D.319, B:Q.375
- Salt bridges: B:R.164, B:H.215, B:H.215, B:K.312, B:R.366
DCP.24: 13 residues within 4Å:- Chain D: Q.149, L.150, R.164, H.210, H.215, K.312, Y.315, D.319, R.366, Y.374
- Ligands: FE.21, MG.22, MG.23
13 PLIP interactions:13 interactions with chain D- Hydrophobic interactions: D:L.150, D:Y.374
- Hydrogen bonds: D:Q.149, D:R.164, D:H.210, D:D.319, D:Y.374, D:Q.375
- Salt bridges: D:R.164, D:H.215, 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
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-tetramer
- Ligands
- 4 x FE: FE (III) ION(Non-covalent)
- 10 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 4 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)
- 4 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 2 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)
- 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
AB
BC
CD
D