- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.35 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x NI: NICKEL (II) ION(Non-covalent)
- 4 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)
DGT.2: 13 residues within 4Å:- Chain A: K.38, V.39, F.40, I.59, N.60, Q.65, R.68, F.88
- Chain B: F.78, T.79, R.350, K.354, K.446
20 PLIP interactions:11 interactions with chain B, 9 interactions with chain A- Hydrogen bonds: B:R.350, A:N.60, A:N.60, A:N.60, A:Q.65, A:R.68
- Water bridges: B:R.350, B:R.350, B:R.350, B:R.350, B:K.354, B:K.354
- Salt bridges: B:R.350, B:K.354, B:K.446, A:K.38, A:K.38, A:K.38
- pi-Cation interactions: B:R.350
- Hydrophobic interactions: A:F.40
DGT.5: 15 residues within 4Å:- Chain A: F.78, T.79, V.271, R.350, K.354
- Chain B: K.38, V.39, F.40, L.56, I.59, N.60, Q.65, R.68, F.88
- Ligands: TTP.6
22 PLIP interactions:11 interactions with chain A, 11 interactions with chain B- Water bridges: A:R.350, A:R.350, A:K.354, A:K.446, A:K.446
- Salt bridges: A:R.350, A:K.354, A:K.354, A:K.446, A:K.446, B:K.38, B:K.38, B:K.38
- pi-Cation interactions: A:R.350
- Hydrophobic interactions: B:F.40
- Hydrogen bonds: B:K.38, B:K.38, B:N.60, B:N.60, B:N.60, B:Q.65, B:R.68
DGT.11: 14 residues within 4Å:- Chain C: K.38, V.39, F.40, I.59, N.60, Q.65, R.68, F.88
- Chain D: F.78, T.79, V.271, R.350, K.354, K.446
21 PLIP interactions:10 interactions with chain C, 11 interactions with chain D- Hydrophobic interactions: C:F.40
- Hydrogen bonds: C:N.60, C:N.60, C:N.60, C:Q.65, C:R.68, D:R.350
- Water bridges: C:R.41, D:R.350, D:R.350, D:K.354, D:K.354, D:K.446
- Salt bridges: C:K.38, C:K.38, C:K.38, D:R.350, D:K.354, D:K.354, D:K.446
- pi-Cation interactions: D:R.350
DGT.14: 16 residues within 4Å:- Chain C: F.78, T.79, V.271, R.350, K.354, K.446
- Chain D: K.38, V.39, F.40, L.56, I.59, N.60, Q.65, R.68, F.88
- Ligands: TTP.15
18 PLIP interactions:11 interactions with chain D, 7 interactions with chain C- Hydrophobic interactions: D:F.40
- Hydrogen bonds: D:K.38, D:K.38, D:N.60, D:N.60, D:N.60, D:Q.65, D:R.68
- Salt bridges: D:K.38, D:K.38, D:K.38, C:R.350, C:K.354, C:K.354, C:K.446
- Water bridges: C:R.350, C:R.350
- pi-Cation interactions: C:R.350
- 3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
TRS.3: 4 residues within 4Å:- Chain A: D.342, R.346, F.380, Y.385
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:R.346, A:R.346, A:Y.385, A:Y.385
- Water bridges: A:D.342, A:G.379
TRS.8: 3 residues within 4Å:- Chain B: D.342, F.380, Y.385
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Y.385
- Water bridges: B:K.345
TRS.9: 4 residues within 4Å:- Chain B: Q.159, F.312, T.313, L.314
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:F.312
- Water bridges: B:Q.159, B:L.314
- 2 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)
TTP.6: 12 residues within 4Å:- Chain A: T.79, F.80, T.221, Q.265, H.269
- Chain B: V.39, F.40, R.41
- Chain D: R.230, R.233, N.247
- Ligands: DGT.5
14 PLIP interactions:9 interactions with chain D, 2 interactions with chain A, 3 interactions with chain B- Hydrogen bonds: D:R.230, B:R.41, B:R.41
- Water bridges: D:R.230, D:R.230, D:R.230, D:R.233, D:R.233, B:Y.47
- Salt bridges: D:R.230, D:R.233, A:H.269
- pi-Cation interactions: D:R.230
- Hydrophobic interactions: A:F.80
TTP.15: 12 residues within 4Å:- Chain B: R.230, R.233, N.247
- Chain C: T.79, F.80, Q.265, H.269
- Chain D: K.38, V.39, F.40, R.41
- Ligands: DGT.14
20 PLIP interactions:3 interactions with chain D, 13 interactions with chain B, 4 interactions with chain C- Hydrogen bonds: D:R.41, D:R.41
- Salt bridges: D:K.38, B:R.230, B:R.233, B:R.233, C:H.269
- Water bridges: B:R.230, B:R.230, B:R.230, B:R.230, B:R.230, B:R.230, B:R.233, B:R.233, B:N.247, C:H.269, C:H.269
- pi-Cation interactions: B:R.230
- Hydrophobic interactions: C:F.80
- 2 x MLI: MALONATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Vorontsov, I.I. et al., Mechanisms of Allosteric Activation and Inhibition of the Deoxyribonucleoside Triphosphate Triphosphohydrolase from Enterococcus faecalis. J.Biol.Chem. (2014)
- Release Date
- 2013-11-20
- Peptides
- HD domain protein: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.35 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x NI: NICKEL (II) ION(Non-covalent)
- 4 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 2 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)
- 2 x MLI: MALONATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Vorontsov, I.I. et al., Mechanisms of Allosteric Activation and Inhibition of the Deoxyribonucleoside Triphosphate Triphosphohydrolase from Enterococcus faecalis. J.Biol.Chem. (2014)
- Release Date
- 2013-11-20
- Peptides
- HD domain protein: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D