- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.95 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x FE2: FE (II) ION(Non-covalent)
- 4 x CL: CHLORIDE ION(Non-functional Binders)
CL.2: 6 residues within 4Å:- Chain A: R.243, H.248, Y.257, R.293, W.304
- Ligands: XXP.3
Ligand excluded by PLIPCL.7: 4 residues within 4Å:- Chain B: R.243, H.248, R.293
- Ligands: XX3.9
Ligand excluded by PLIPCL.17: 5 residues within 4Å:- Chain C: R.243, H.248, Y.257, R.293
- Ligands: XX2.18
Ligand excluded by PLIPCL.24: 6 residues within 4Å:- Chain D: R.243, H.248, Y.257, R.293, W.304
- Ligands: XX3.25
Ligand excluded by PLIP- 1 x XXP: 2-KETO,5-NITRO,6-HYDROXY-3,5-HEXADIENOIC ACID(Non-covalent)
XXP.3: 17 residues within 4Å:- Chain A: H.155, N.157, W.192, H.200, H.214, R.243, H.248, V.250, S.251, Y.257, E.267, Y.269, R.292, R.293, W.304
- Ligands: FE2.1, CL.2
9 PLIP interactions:9 interactions with chain A- Hydrophobic interactions: A:W.192
- Hydrogen bonds: A:N.157, A:Y.257, A:R.292, A:R.293
- Salt bridges: A:H.155, A:H.200, A:H.214, A:H.248
- 13 x GOL: GLYCEROL(Non-functional Binders)
GOL.4: 7 residues within 4Å:- Chain A: R.243, G.244, Y.255, N.298, P.299, V.301
- Chain C: N.298
4 PLIP interactions:1 interactions with chain C, 3 interactions with chain A- Hydrogen bonds: C:N.298, A:G.244, A:Y.255
- Water bridges: A:N.298
GOL.5: 3 residues within 4Å:- Chain A: I.283, T.284, W.285
4 PLIP interactions:2 interactions with chain A, 2 interactions with chain C- Hydrogen bonds: A:T.284, C:R.236
- Water bridges: A:N.286, C:R.236
GOL.10: 6 residues within 4Å:- Chain B: R.243, G.244, N.298, P.299, V.301
- Chain D: N.298
5 PLIP interactions:4 interactions with chain B, 1 interactions with chain D- Hydrogen bonds: B:G.244, B:Y.255, B:Y.255, B:N.298, D:N.298
GOL.11: 6 residues within 4Å:- Chain B: D.289, F.341, T.342, R.343, A.344
- Chain D: R.236
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:D.289, B:A.344
GOL.12: 3 residues within 4Å:- Chain B: K.75, R.104, F.108
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:K.75, B:R.104, B:F.108
- Water bridges: B:R.117, B:R.117, B:D.315
GOL.13: 3 residues within 4Å:- Chain B: I.283, T.284, W.285
3 PLIP interactions:1 interactions with chain D, 2 interactions with chain B- Water bridges: D:R.236, B:N.286
- Hydrogen bonds: B:T.284
GOL.14: 5 residues within 4Å:- Chain B: A.12, P.13, D.14, G.174, R.195
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:R.195
- Water bridges: B:A.12
GOL.15: 5 residues within 4Å:- Chain B: S.44, Y.45, H.61, K.110, T.133
1 PLIP interactions:1 interactions with chain B- Water bridges: B:S.44
GOL.20: 7 residues within 4Å:- Chain A: N.298
- Chain C: R.243, G.244, Y.255, N.298, P.299, V.301
5 PLIP interactions:4 interactions with chain C, 1 interactions with chain A- Hydrogen bonds: C:G.244, C:Y.255, C:Y.255, A:N.298
- Water bridges: C:N.298
GOL.21: 6 residues within 4Å:- Chain C: V.24, T.67, K.68, G.69, K.75, L.312
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:K.68, C:K.75
GOL.22: 3 residues within 4Å:- Chain C: I.283, T.284, W.285
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:T.284
- Water bridges: C:N.286
GOL.26: 8 residues within 4Å:- Chain B: N.298
- Chain D: R.243, G.244, Y.255, D.294, N.298, P.299, V.301
5 PLIP interactions:4 interactions with chain D, 1 interactions with chain B- Hydrogen bonds: D:G.244, D:Y.255, D:D.294, B:N.298
- Water bridges: D:N.298
GOL.27: 5 residues within 4Å:- Chain D: T.26, D.27, K.30, P.261, D.262
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:T.26
- Water bridges: D:T.26, D:D.27
- 1 x CA: CALCIUM ION(Non-covalent)
- 2 x XX3: (1S)-1-HYDROPEROXY-1-HYDROXY-2-KETO-5-NITROCYCLOHEXA-3,5-DIENE(Non-covalent)
XX3.9: 17 residues within 4Å:- Chain B: H.155, N.157, W.192, H.200, H.214, R.243, H.248, V.250, S.251, Y.257, E.267, Y.269, R.292, R.293, W.304
- Ligands: FE2.6, CL.7
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:V.250
- Hydrogen bonds: B:N.157, B:Y.257
XX3.25: 17 residues within 4Å:- Chain D: H.155, N.157, W.192, H.200, H.214, R.243, H.248, V.250, S.251, Y.257, E.267, Y.269, R.292, R.293, W.304
- Ligands: FE2.23, CL.24
2 PLIP interactions:2 interactions with chain D- Hydrophobic interactions: D:V.250
- Hydrogen bonds: D:N.157
- 1 x XX2: 1-KETO,2-HYDROXY,4-NITROBENZENE, 1 ELECTRON OXIDIZED(Non-covalent)
- 1 x OXY: OXYGEN MOLECULE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kovaleva, E.G. et al., Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates. Science (2007)
- Release Date
- 2007-04-24
- Peptides
- Homoprotocatechuate 2,3-dioxygenase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.95 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x FE2: FE (II) ION(Non-covalent)
- 4 x CL: CHLORIDE ION(Non-functional Binders)
- 1 x XXP: 2-KETO,5-NITRO,6-HYDROXY-3,5-HEXADIENOIC ACID(Non-covalent)
- 13 x GOL: GLYCEROL(Non-functional Binders)
- 1 x CA: CALCIUM ION(Non-covalent)
- 2 x XX3: (1S)-1-HYDROPEROXY-1-HYDROXY-2-KETO-5-NITROCYCLOHEXA-3,5-DIENE(Non-covalent)
- 1 x XX2: 1-KETO,2-HYDROXY,4-NITROBENZENE, 1 ELECTRON OXIDIZED(Non-covalent)
- 1 x OXY: OXYGEN MOLECULE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kovaleva, E.G. et al., Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates. Science (2007)
- Release Date
- 2007-04-24
- Peptides
- Homoprotocatechuate 2,3-dioxygenase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D