- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.85 Å
- Oligo State
- homo-pentamer
- Ligands
- 5 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 15 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.2: 8 residues within 4Å:- Chain A: T.112, Y.113, W.148, W.149, F.189
- Chain C: R.206
- Ligands: HEM.1, PO4.3
5 PLIP interactions:2 interactions with chain A, 3 interactions with chain C- Hydrogen bonds: A:Y.113, A:Y.113
- Water bridges: C:R.206, C:R.206
- Salt bridges: C:R.206
PO4.3: 6 residues within 4Å:- Chain A: K.109, H.180, F.189
- Chain C: H.202, R.206
- Ligands: PO4.2
4 PLIP interactions:2 interactions with chain C, 2 interactions with chain A- Water bridges: C:R.206
- Salt bridges: C:H.202, A:K.109, A:H.180
PO4.4: 4 residues within 4Å:- Chain A: K.143, R.218, R.219
- Chain C: H.222
6 PLIP interactions:5 interactions with chain A, 1 interactions with chain C- Water bridges: A:K.143, A:K.143, A:R.219
- Salt bridges: A:K.143, A:R.218, C:H.222
PO4.9: 6 residues within 4Å:- Chain B: H.202, R.206
- Chain C: K.109, H.180, F.189
- Ligands: PO4.16
3 PLIP interactions:1 interactions with chain B, 2 interactions with chain C- Salt bridges: B:H.202, C:H.180
- Water bridges: C:T.182
PO4.10: 9 residues within 4Å:- Chain B: T.112, Y.113, W.148, W.149, R.156, F.189
- Chain D: R.206
- Ligands: HEM.8, PO4.22
4 PLIP interactions:2 interactions with chain B, 2 interactions with chain D- Hydrogen bonds: B:T.112
- Water bridges: B:T.112, D:R.206
- Salt bridges: D:R.206
PO4.11: 4 residues within 4Å:- Chain B: K.143, R.218, R.219
- Chain D: H.222
3 PLIP interactions:1 interactions with chain D, 2 interactions with chain B- Salt bridges: D:H.222, B:K.143, B:R.218
PO4.16: 8 residues within 4Å:- Chain B: R.206
- Chain C: T.112, Y.113, W.148, W.149, F.189
- Ligands: PO4.9, HEM.15
6 PLIP interactions:3 interactions with chain C, 3 interactions with chain B- Hydrogen bonds: C:Y.113, C:Y.113, C:R.156
- Water bridges: B:R.206, B:R.206
- Salt bridges: B:R.206
PO4.17: 4 residues within 4Å:- Chain B: H.222
- Chain C: K.143, R.218, R.219
4 PLIP interactions:2 interactions with chain C, 2 interactions with chain B- Water bridges: C:R.219, B:H.222
- Salt bridges: C:K.143, B:H.222
PO4.22: 6 residues within 4Å:- Chain B: K.109, H.180, F.189
- Chain D: H.202, R.206
- Ligands: PO4.10
4 PLIP interactions:2 interactions with chain D, 2 interactions with chain B- Water bridges: D:R.206
- Salt bridges: D:H.202, B:K.109, B:H.180
PO4.23: 8 residues within 4Å:- Chain D: T.112, Y.113, W.148, W.149, F.189
- Chain E: R.206
- Ligands: HEM.21, PO4.29
5 PLIP interactions:3 interactions with chain D, 2 interactions with chain E- Hydrogen bonds: D:T.112
- Water bridges: D:T.112, D:R.156, E:R.206
- Salt bridges: E:R.206
PO4.24: 4 residues within 4Å:- Chain D: K.143, R.218, R.219
- Chain E: H.222
5 PLIP interactions:3 interactions with chain D, 2 interactions with chain E- Water bridges: D:R.219, E:H.222
- Salt bridges: D:K.143, D:R.218, E:H.222
PO4.28: 8 residues within 4Å:- Chain A: R.206
- Chain E: T.112, Y.113, W.148, W.149, F.189
- Ligands: HEM.27, PO4.30
6 PLIP interactions:3 interactions with chain A, 3 interactions with chain E- Water bridges: A:R.206, A:R.206
- Salt bridges: A:R.206
- Hydrogen bonds: E:T.112, E:Y.113, E:Y.113
PO4.29: 6 residues within 4Å:- Chain D: K.109, H.180, F.189
- Chain E: H.202, R.206
- Ligands: PO4.23
4 PLIP interactions:1 interactions with chain E, 3 interactions with chain D- Salt bridges: E:H.202, D:K.109, D:H.180
- Water bridges: D:T.182
PO4.30: 6 residues within 4Å:- Chain A: H.202, R.206
- Chain E: K.109, H.180, F.189
- Ligands: PO4.28
7 PLIP interactions:2 interactions with chain A, 5 interactions with chain E- Water bridges: A:R.206, E:K.109, E:K.109, E:T.182
- Salt bridges: A:H.202, E:K.109, E:H.180
PO4.31: 4 residues within 4Å:- Chain A: H.222
- Chain E: K.143, R.218, R.219
3 PLIP interactions:1 interactions with chain E, 2 interactions with chain A- Water bridges: E:D.186, A:H.222
- Salt bridges: A:H.222
- 5 x IMD: IMIDAZOLE(Non-covalent)
IMD.5: 8 residues within 4Å:- Chain A: R.176, K.177, L.178, T.191, F.193
- Ligands: HEM.1, EDO.6, EDO.7
No protein-ligand interaction detected (PLIP)IMD.12: 7 residues within 4Å:- Chain B: R.176, K.177, L.178, T.191, F.193
- Ligands: HEM.8, EDO.13
No protein-ligand interaction detected (PLIP)IMD.18: 8 residues within 4Å:- Chain C: R.176, K.177, L.178, T.191, F.193
- Ligands: HEM.15, EDO.19, EDO.20
No protein-ligand interaction detected (PLIP)IMD.25: 6 residues within 4Å:- Chain D: R.176, K.177, L.178, F.193
- Ligands: HEM.21, EDO.26
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:K.177
IMD.32: 7 residues within 4Å:- Chain E: R.176, K.177, L.178, F.193
- Ligands: HEM.27, EDO.33, EDO.34
No protein-ligand interaction detected (PLIP)- 9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.6: 5 residues within 4Å:- Chain A: L.125, R.176
- Ligands: HEM.1, IMD.5, EDO.7
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.176
EDO.7: 5 residues within 4Å:- Chain A: R.176, K.177, L.178
- Ligands: IMD.5, EDO.6
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:R.176, A:L.178
- Water bridges: A:K.177, A:K.177, A:K.177, A:L.178
EDO.13: 5 residues within 4Å:- Chain B: R.176, K.177, L.178
- Ligands: IMD.12, EDO.14
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:R.176, B:L.178
- Water bridges: B:R.176, B:K.177, B:K.177, B:K.177, B:L.178
EDO.14: 7 residues within 4Å:- Chain B: K.109, K.110, P.111, L.178, H.180
- Ligands: HEM.8, EDO.13
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:H.180
- Water bridges: B:K.109, B:K.109, B:T.112
EDO.19: 5 residues within 4Å:- Chain C: R.176, K.177, L.178
- Ligands: IMD.18, EDO.20
6 PLIP interactions:6 interactions with chain C- Hydrogen bonds: C:R.176, C:L.178
- Water bridges: C:K.177, C:K.177, C:K.177, C:L.178
EDO.20: 5 residues within 4Å:- Chain C: L.125, R.176
- Ligands: HEM.15, IMD.18, EDO.19
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:R.176
EDO.26: 4 residues within 4Å:- Chain D: R.176, K.177, L.178
- Ligands: IMD.25
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:R.176, D:L.178, D:L.178
EDO.33: 5 residues within 4Å:- Chain E: L.125, R.176
- Ligands: HEM.27, IMD.32, EDO.34
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:R.176
EDO.34: 5 residues within 4Å:- Chain E: R.176, K.177, L.178
- Ligands: IMD.32, EDO.33
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:L.178, E:L.178
- Water bridges: E:K.177
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kostan, J. et al., Structural and functional characterisation of the chlorite dismutase from the nitrite-oxidizing bacterium "Candidatus Nitrospira defluvii": Identification of a catalytically important amino acid residue. J.Struct.Biol. (2010)
- Release Date
- 2010-07-28
- Peptides
- Chlorite dismutase: ABCDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
E
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.85 Å
- Oligo State
- homo-pentamer
- Ligands
- 5 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 15 x PO4: PHOSPHATE ION(Non-functional Binders)
- 5 x IMD: IMIDAZOLE(Non-covalent)
- 9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kostan, J. et al., Structural and functional characterisation of the chlorite dismutase from the nitrite-oxidizing bacterium "Candidatus Nitrospira defluvii": Identification of a catalytically important amino acid residue. J.Struct.Biol. (2010)
- Release Date
- 2010-07-28
- Peptides
- Chlorite dismutase: ABCDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
E