- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.67 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x FE2: FE (II) ION(Non-covalent)
- 3 x 4NC: 4-NITROCATECHOL(Non-covalent)
4NC.2: 15 residues within 4Å:- Chain A: H.155, W.192, H.200, H.214, R.243, H.248, V.250, S.251, F.257, E.267, Y.269, R.292, R.293
- Ligands: FE2.1, CL.4
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:W.192
- Hydrogen bonds: A:V.250
- Water bridges: A:N.157
- pi-Stacking: A:H.248
4NC.12: 16 residues within 4Å:- Chain C: H.155, W.192, H.200, H.214, R.243, H.248, V.250, S.251, F.257, E.267, Y.269, R.292, R.293
- Ligands: FE2.11, OXY.15, CL.16
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:W.192
- Hydrogen bonds: C:V.250
- Water bridges: C:N.157
- pi-Stacking: C:H.248
4NC.18: 16 residues within 4Å:- Chain D: H.155, W.192, H.200, H.214, R.243, H.248, V.250, S.251, F.257, E.267, Y.269, R.292, R.293
- Ligands: FE2.17, OXY.20, CL.21
5 PLIP interactions:5 interactions with chain D- Hydrophobic interactions: D:H.248, D:V.250
- Hydrogen bonds: D:V.250
- Water bridges: D:N.157
- pi-Stacking: D:H.248
- 5 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)
P6G.3: 14 residues within 4Å:- Chain A: E.22, V.24, T.67, K.68, G.69, K.75, R.104, F.108, V.109, R.117, L.312, L.314, D.315, G.316
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:E.22, A:K.75
- Water bridges: A:Q.50, A:R.117
P6G.9: 11 residues within 4Å:- Chain B: E.22, V.24, T.67, K.68, K.75, R.104, F.108, R.117, L.312, D.315, G.316
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:E.22, B:K.75
- Water bridges: B:R.117
P6G.10: 6 residues within 4Å:- Chain B: Q.182, D.183, D.184, T.284, A.344, G.345
1 PLIP interactions:1 interactions with chain B- Water bridges: B:N.286
P6G.14: 12 residues within 4Å:- Chain C: E.22, V.24, T.67, K.68, G.69, K.75, R.104, F.108, R.117, L.312, D.315, G.316
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:E.22, C:K.75
- Water bridges: C:Q.50, C:R.117
P6G.19: 11 residues within 4Å:- Chain D: E.22, V.24, T.67, K.68, K.75, R.104, F.108, R.117, L.312, D.315, G.316
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:E.22, D:K.75
- Water bridges: D:Q.50, D:R.117
- 4 x CL: CHLORIDE ION(Non-functional Binders)
CL.4: 5 residues within 4Å:- Chain A: R.243, H.248, R.293, W.304
- Ligands: 4NC.2
Ligand excluded by PLIPCL.6: 3 residues within 4Å:- Chain B: R.243, H.248, R.293
Ligand excluded by PLIPCL.16: 5 residues within 4Å:- Chain C: R.243, H.248, R.293, W.304
- Ligands: 4NC.12
Ligand excluded by PLIPCL.21: 5 residues within 4Å:- Chain D: R.243, H.248, R.293, W.304
- Ligands: 4NC.18
Ligand excluded by PLIP- 1 x CA: CALCIUM ION(Non-covalent)
- 2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
PG4.8: 8 residues within 4Å:- Chain A: R.82
- Chain B: A.12, D.14, R.82, D.172, L.173, G.174, R.195
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:R.82, B:D.172, B:R.195, B:R.195, B:R.195
PG4.13: 7 residues within 4Å:- Chain C: A.12, D.14, D.172, L.173, G.174, R.195
- Chain D: R.82
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:R.195, C:R.195, C:R.195
- 2 x OXY: OXYGEN MOLECULE(Non-covalent)
OXY.15: 8 residues within 4Å:- Chain C: H.155, N.157, W.192, H.200, A.203, H.214
- Ligands: FE2.11, 4NC.12
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:F.156, C:N.157
OXY.20: 8 residues within 4Å:- Chain D: H.155, N.157, W.192, H.200, A.203, H.214
- Ligands: FE2.17, 4NC.18
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:F.156, D:N.157
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kovaleva, E.G. et al., Structural basis for the role of tyrosine 257 of homoprotocatechuate 2,3-dioxygenase in substrate and oxygen activation. Biochemistry (2012)
- Release Date
- 2012-10-31
- 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 1.67 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x FE2: FE (II) ION(Non-covalent)
- 3 x 4NC: 4-NITROCATECHOL(Non-covalent)
- 5 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)
- 4 x CL: CHLORIDE ION(Non-functional Binders)
- 1 x CA: CALCIUM ION(Non-covalent)
- 2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 2 x OXY: OXYGEN MOLECULE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kovaleva, E.G. et al., Structural basis for the role of tyrosine 257 of homoprotocatechuate 2,3-dioxygenase in substrate and oxygen activation. Biochemistry (2012)
- Release Date
- 2012-10-31
- Peptides
- Homoprotocatechuate 2,3-dioxygenase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D