- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.33 Å
- Oligo State
- homo-tetramer
- Ligands
- 3 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)
- 5 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)
DGT.2: 16 residues within 4Å:- Chain A: Y.43, V.44, V.266, R.339, K.343
- Chain C: K.411
- Chain D: K.4, V.5, I.6, I.24, D.25, Q.30, R.33, F.53
- Ligands: DTP.9, MG.13
17 PLIP interactions:10 interactions with chain D, 5 interactions with chain A, 2 interactions with chain C- Hydrogen bonds: D:Q.30, D:R.33
- Water bridges: D:K.4, D:K.4, D:K.4, D:K.4
- Salt bridges: D:K.4, D:K.4, D:K.4, D:D.25, A:K.265, A:R.339, A:K.343, A:K.343, C:K.411, C:K.411
- pi-Cation interactions: A:R.339
DGT.6: 16 residues within 4Å:- Chain B: Y.43, V.44, V.266, R.339, K.343
- Chain C: K.4, V.5, I.6, I.24, D.25, Q.30, R.33, F.53
- Chain D: K.411
- Ligands: MG.10, DTP.14
18 PLIP interactions:9 interactions with chain C, 3 interactions with chain D, 6 interactions with chain B- Hydrophobic interactions: C:I.6
- Hydrogen bonds: C:Q.30, C:R.33, B:R.339
- Water bridges: C:K.4, C:K.4, D:K.411, B:K.265
- Salt bridges: C:K.4, C:K.4, C:K.4, C:D.25, D:K.411, D:K.411, B:R.339, B:K.343, B:K.343
- pi-Cation interactions: B:R.339
DGT.11: 16 residues within 4Å:- Chain C: Q.37, L.38, R.52, R.94, H.98, H.103, H.121, D.199, K.200, Y.203, D.207, R.254, H.258, Y.262, Q.263, D.271
18 PLIP interactions:18 interactions with chain C- Hydrophobic interactions: C:L.38, C:Y.262
- Hydrogen bonds: C:Q.37, C:L.38, C:R.52, C:R.94, C:Q.263
- Salt bridges: C:R.52, C:R.94, C:H.98, C:H.103, C:H.103, C:H.121, C:H.121, C:K.200, C:R.254, C:D.271
- pi-Stacking: C:H.103
DGT.12: 16 residues within 4Å:- Chain A: K.411
- Chain B: K.4, V.5, I.6, I.24, D.25, Q.30, R.33, F.53
- Chain C: Y.43, V.44, V.266, R.339, K.343
- Ligands: DTP.3, MG.7
16 PLIP interactions:5 interactions with chain C, 9 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: C:R.339, B:Q.30, B:R.33
- Salt bridges: C:R.339, C:K.343, C:K.343, B:K.4, B:K.4, B:K.4, B:D.25, A:K.411, A:K.411
- pi-Cation interactions: C:R.339
- Hydrophobic interactions: B:I.6
- Water bridges: B:K.4, B:K.4
DGT.16: 16 residues within 4Å:- Chain A: K.4, V.5, I.6, I.24, D.25, Q.30, R.33, F.53
- Chain B: K.411
- Chain D: Y.43, V.44, V.266, R.339, K.343
- Ligands: MG.4, DTP.8
18 PLIP interactions:6 interactions with chain D, 10 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: D:R.339, A:Q.30, A:R.33
- Salt bridges: D:K.265, D:R.339, D:K.343, D:K.343, A:K.4, A:K.4, A:K.4, A:D.25, B:K.411, B:K.411
- pi-Cation interactions: D:R.339
- Hydrophobic interactions: A:I.6
- Water bridges: A:K.4, A:K.4, A:V.5
- 4 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)
DTP.3: 17 residues within 4Å:- Chain A: R.221, R.240, K.242, N.246, K.411
- Chain B: V.5, I.6, N.7, H.13
- Chain C: V.44, F.45, R.260, H.264, K.265, V.266
- Ligands: MG.7, DGT.12
23 PLIP interactions:14 interactions with chain A, 7 interactions with chain C, 2 interactions with chain B- Hydrogen bonds: A:R.221, A:N.246, A:N.246, B:N.7, B:N.7
- Water bridges: A:R.240, A:K.411, A:K.411
- Salt bridges: A:R.221, A:R.240, A:K.242, A:K.242, A:K.242, A:K.411, C:H.264, C:H.264, C:K.265, C:K.265, C:K.265
- pi-Cation interactions: A:R.221, A:R.221
- Hydrophobic interactions: C:V.44, C:F.45
DTP.8: 18 residues within 4Å:- Chain A: V.5, I.6, N.7, H.13
- Chain B: R.221, F.225, R.240, K.242, N.246, K.411
- Chain D: V.44, F.45, R.260, H.264, K.265, V.266
- Ligands: MG.4, DGT.16
22 PLIP interactions:13 interactions with chain B, 7 interactions with chain D, 2 interactions with chain A- Hydrogen bonds: B:R.221, B:N.246, B:N.246, A:N.7, A:N.7
- Water bridges: B:K.242, B:K.242
- Salt bridges: B:R.221, B:R.240, B:K.242, B:K.242, B:K.242, B:K.411, D:H.264, D:H.264, D:K.265, D:K.265, D:K.265
- pi-Cation interactions: B:R.221, B:R.221
- Hydrophobic interactions: D:V.44, D:F.45
DTP.9: 18 residues within 4Å:- Chain A: V.44, F.45, R.260, H.264, K.265, V.266
- Chain C: R.221, F.225, R.240, K.242, N.246, K.411
- Chain D: V.5, I.6, N.7, H.13
- Ligands: DGT.2, MG.13
21 PLIP interactions:12 interactions with chain C, 2 interactions with chain D, 7 interactions with chain A- Hydrogen bonds: C:R.221, C:N.246, C:N.246, D:N.7, D:N.7
- Water bridges: C:R.240
- Salt bridges: C:R.221, C:R.240, C:K.242, C:K.242, C:K.242, C:K.411, A:H.264, A:H.264, A:K.265, A:K.265, A:K.265
- pi-Cation interactions: C:R.221, C:R.221
- Hydrophobic interactions: A:V.44, A:F.45
DTP.14: 18 residues within 4Å:- Chain B: V.44, F.45, R.260, H.264, K.265, V.266
- Chain C: V.5, I.6, N.7, H.13
- Chain D: R.221, F.225, R.240, K.242, N.246, K.411
- Ligands: DGT.6, MG.10
22 PLIP interactions:11 interactions with chain D, 9 interactions with chain B, 2 interactions with chain C- Hydrogen bonds: D:R.221, D:N.246, D:N.246, C:N.7, C:N.7
- Salt bridges: D:R.221, D:R.240, D:K.242, D:K.242, D:K.242, D:K.411, B:H.264, B:H.264, B:K.265, B:K.265, B:K.265
- pi-Cation interactions: D:R.221, D:R.221
- Hydrophobic interactions: B:V.44, B:F.45
- Water bridges: B:K.265, B:K.265
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.4: 4 residues within 4Å:- Chain A: K.4
- Chain B: K.411
- Ligands: DTP.8, DGT.16
No protein-ligand interaction detected (PLIP)MG.7: 4 residues within 4Å:- Chain A: K.411
- Chain B: K.4
- Ligands: DTP.3, DGT.12
No protein-ligand interaction detected (PLIP)MG.10: 4 residues within 4Å:- Chain C: K.4
- Chain D: K.411
- Ligands: DGT.6, DTP.14
No protein-ligand interaction detected (PLIP)MG.13: 4 residues within 4Å:- Chain C: K.411
- Chain D: K.4
- Ligands: DGT.2, DTP.9
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ji, X. et al., Structural basis of cellular dNTP regulation by SAMHD1. Proc.Natl.Acad.Sci.USA (2014)
- Release Date
- 2014-10-01
- Peptides
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.33 Å
- Oligo State
- homo-tetramer
- Ligands
- 3 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)
- 5 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 4 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ji, X. et al., Structural basis of cellular dNTP regulation by SAMHD1. Proc.Natl.Acad.Sci.USA (2014)
- Release Date
- 2014-10-01
- Peptides
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D