- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x FMT: FORMIC ACID(Non-functional Binders)
- 6 x GOL: GLYCEROL(Non-functional Binders)
GOL.5: 8 residues within 4Å:- Chain A: Y.72, N.80, H.99, H.101
- Chain D: I.84, Q.87
- Ligands: NI.6, GOL.19
3 PLIP interactions:1 interactions with chain D, 2 interactions with chain A- Hydrogen bonds: D:Q.87, A:Y.72, A:H.99
GOL.7: 4 residues within 4Å:- Chain B: H.75, E.104, H.105
- Ligands: CIT.9
No protein-ligand interaction detected (PLIP)GOL.8: 8 residues within 4Å:- Chain B: N.80, M.83, Q.87, T.97, E.109, I.111
- Chain C: N.80
- Ligands: GOL.16
5 PLIP interactions:1 interactions with chain C, 4 interactions with chain B- Water bridges: C:N.80
- Hydrogen bonds: B:N.80, B:M.83, B:T.97, B:T.97
GOL.16: 8 residues within 4Å:- Chain B: I.84, Q.87
- Chain C: Y.72, N.80, H.99, H.101
- Ligands: GOL.8, NI.17
4 PLIP interactions:2 interactions with chain B, 2 interactions with chain C- Hydrogen bonds: B:Q.87, C:Y.72, C:Y.72
- Water bridges: B:T.97
GOL.18: 4 residues within 4Å:- Chain D: H.75, E.104, H.105
- Ligands: CIT.20
No protein-ligand interaction detected (PLIP)GOL.19: 8 residues within 4Å:- Chain A: N.80
- Chain D: N.80, M.83, Q.87, T.97, E.109, I.111
- Ligands: GOL.5
4 PLIP interactions:3 interactions with chain D, 1 interactions with chain A- Hydrogen bonds: D:N.80, D:M.83, D:T.97
- Water bridges: A:N.80
- 6 x NI: NICKEL (II) ION(Non-covalent)
NI.6: 4 residues within 4Å:- Chain A: H.74, H.101
- Chain D: H.88
- Ligands: GOL.5
6 PLIP interactions:2 interactions with chain A, 1 interactions with chain D, 3 Ligand-Water interactions- Metal complexes: A:H.74, A:H.101, D:H.88, H2O.22, H2O.62, H2O.209
NI.10: 5 residues within 4Å:- Chain B: H.99, H.101, C.107
- Chain C: I.84, H.88
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain C- Metal complexes: B:H.99, B:H.101, B:C.107, C:H.88
NI.11: 5 residues within 4Å:- Chain B: H.74, H.75, E.104
- Chain C: H.88
- Ligands: CIT.9
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:H.74, B:H.75, B:E.104
NI.17: 4 residues within 4Å:- Chain B: H.88
- Chain C: H.74, H.101
- Ligands: GOL.16
6 PLIP interactions:2 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: C:H.74, C:H.101, B:H.88, H2O.91, H2O.140, H2O.180
NI.21: 5 residues within 4Å:- Chain A: I.84, H.88
- Chain D: H.99, H.101, C.107
4 PLIP interactions:1 interactions with chain A, 3 interactions with chain D- Metal complexes: A:H.88, D:H.99, D:H.101, D:C.107
NI.22: 5 residues within 4Å:- Chain A: H.88
- Chain D: H.74, H.75, E.104
- Ligands: CIT.20
3 PLIP interactions:3 interactions with chain D- Metal complexes: D:H.74, D:H.75, D:E.104
- 2 x CIT: CITRIC ACID(Non-functional Binders)
CIT.9: 8 residues within 4Å:- Chain B: H.74, H.75, D.103, E.104
- Chain C: H.88, A.89
- Ligands: GOL.7, NI.11
7 PLIP interactions:4 interactions with chain B, 3 interactions with chain C- Salt bridges: B:H.74, B:H.74, B:H.75, B:H.75, C:H.88
- Water bridges: C:D.85, C:A.89
CIT.20: 8 residues within 4Å:- Chain A: H.88, A.89
- Chain D: H.74, H.75, D.103, E.104
- Ligands: GOL.18, NI.22
7 PLIP interactions:3 interactions with chain A, 4 interactions with chain D- Water bridges: A:A.89, A:A.89
- Salt bridges: A:H.88, D:H.74, D:H.74, D:H.75, D:H.75
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Dian, C. et al., Structural Basis of the Nickel Response in Helicobacter Pylori: Crystal Structures of Hpnikr in Apo and Nickel-Bound States. J.Mol.Biol. (2006)
- Release Date
- 2006-07-17
- Peptides
- PUTATIVE NICKEL-RESPONSIVE REGULATOR: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x FMT: FORMIC ACID(Non-functional Binders)
- 6 x GOL: GLYCEROL(Non-functional Binders)
- 6 x NI: NICKEL (II) ION(Non-covalent)
- 2 x CIT: CITRIC ACID(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Dian, C. et al., Structural Basis of the Nickel Response in Helicobacter Pylori: Crystal Structures of Hpnikr in Apo and Nickel-Bound States. J.Mol.Biol. (2006)
- Release Date
- 2006-07-17
- Peptides
- PUTATIVE NICKEL-RESPONSIVE REGULATOR: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B