- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-octamer
- Ligands
- 8 x MG: MAGNESIUM ION(Non-covalent)
- 8 x FE2: FE (II) ION(Non-covalent)
FE2.2: 6 residues within 4Å:- Chain A: H.152, H.215, Y.256, E.266
- Ligands: BPY.3, GOL.7
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:H.152, A:H.215, A:E.266, H2O.1, H2O.2
FE2.9: 6 residues within 4Å:- Chain B: H.152, H.215, Y.256, E.266
- Ligands: BPY.10, GOL.14
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:H.152, B:H.215, B:E.266, H2O.203, H2O.204
FE2.16: 6 residues within 4Å:- Chain C: H.152, H.215, Y.256, E.266
- Ligands: BPY.17, GOL.21
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:H.152, C:H.215, C:E.266, H2O.405, H2O.406
FE2.23: 6 residues within 4Å:- Chain D: H.152, H.215, Y.256, E.266
- Ligands: BPY.24, GOL.28
5 PLIP interactions:3 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:H.152, D:H.215, D:E.266, H2O.607, H2O.608
FE2.30: 6 residues within 4Å:- Chain E: H.152, H.215, Y.256, E.266
- Ligands: BPY.31, GOL.35
5 PLIP interactions:3 interactions with chain E, 2 Ligand-Water interactions- Metal complexes: E:H.152, E:H.215, E:E.266, H2O.809, H2O.810
FE2.37: 6 residues within 4Å:- Chain F: H.152, H.215, Y.256, E.266
- Ligands: BPY.38, GOL.42
5 PLIP interactions:3 interactions with chain F, 2 Ligand-Water interactions- Metal complexes: F:H.152, F:H.215, F:E.266, H2O.1011, H2O.1012
FE2.44: 6 residues within 4Å:- Chain G: H.152, H.215, Y.256, E.266
- Ligands: BPY.45, GOL.49
5 PLIP interactions:3 interactions with chain G, 2 Ligand-Water interactions- Metal complexes: G:H.152, G:H.215, G:E.266, H2O.1213, H2O.1214
FE2.51: 6 residues within 4Å:- Chain H: H.152, H.215, Y.256, E.266
- Ligands: BPY.52, GOL.56
5 PLIP interactions:3 interactions with chain H, 2 Ligand-Water interactions- Metal complexes: H:H.152, H:H.215, H:E.266, H2O.1415, H2O.1416
- 24 x BPY: BIPHENYL-2,3-DIOL(Non-covalent)
BPY.3: 14 residues within 4Å:- Chain A: H.152, I.154, L.190, F.192, H.200, H.215, H.247, N.249, D.250, Y.256, E.266, L.297
- Ligands: FE2.2, GOL.7
9 PLIP interactions:9 interactions with chain A- Hydrophobic interactions: A:I.154, A:L.190, A:F.192, A:F.192, A:H.247, A:L.297
- Hydrogen bonds: A:D.250
- pi-Stacking: A:H.247
- pi-Cation interactions: A:H.215
BPY.4: 7 residues within 4Å:- Chain A: G.171, R.173, H.194, C.195, N.196, A.197, D.276
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:A.197
- Hydrogen bonds: A:D.276
- pi-Stacking: A:H.194
BPY.5: 7 residues within 4Å:- Chain A: A.22, S.25, F.26, M.30, I.238, T.259, P.260
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:F.26, A:I.238, A:I.238, A:P.260
BPY.10: 14 residues within 4Å:- Chain B: H.152, I.154, L.190, F.192, H.200, H.215, H.247, N.249, D.250, Y.256, E.266, L.297
- Ligands: FE2.9, GOL.14
9 PLIP interactions:9 interactions with chain B- Hydrophobic interactions: B:I.154, B:L.190, B:F.192, B:F.192, B:H.247, B:L.297
- Hydrogen bonds: B:D.250
- pi-Stacking: B:H.247
- pi-Cation interactions: B:H.215
BPY.11: 7 residues within 4Å:- Chain B: G.171, R.173, H.194, C.195, N.196, A.197, D.276
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:A.197
- Hydrogen bonds: B:D.276
- pi-Stacking: B:H.194
BPY.12: 7 residues within 4Å:- Chain B: A.22, S.25, F.26, M.30, I.238, T.259, P.260
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:F.26, B:I.238, B:I.238, B:P.260
BPY.17: 14 residues within 4Å:- Chain C: H.152, I.154, L.190, F.192, H.200, H.215, H.247, N.249, D.250, Y.256, E.266, L.297
- Ligands: FE2.16, GOL.21
9 PLIP interactions:9 interactions with chain C- Hydrophobic interactions: C:I.154, C:L.190, C:F.192, C:F.192, C:H.247, C:L.297
- Hydrogen bonds: C:D.250
- pi-Stacking: C:H.247
- pi-Cation interactions: C:H.215
BPY.18: 7 residues within 4Å:- Chain C: G.171, R.173, H.194, C.195, N.196, A.197, D.276
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:A.197
- Hydrogen bonds: C:D.276
- pi-Stacking: C:H.194
BPY.19: 7 residues within 4Å:- Chain C: A.22, S.25, F.26, M.30, I.238, T.259, P.260
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:F.26, C:I.238, C:I.238, C:P.260
BPY.24: 14 residues within 4Å:- Chain D: H.152, I.154, L.190, F.192, H.200, H.215, H.247, N.249, D.250, Y.256, E.266, L.297
- Ligands: FE2.23, GOL.28
9 PLIP interactions:9 interactions with chain D- Hydrophobic interactions: D:I.154, D:L.190, D:F.192, D:F.192, D:H.247, D:L.297
- Hydrogen bonds: D:D.250
- pi-Stacking: D:H.247
- pi-Cation interactions: D:H.215
BPY.25: 7 residues within 4Å:- Chain D: G.171, R.173, H.194, C.195, N.196, A.197, D.276
3 PLIP interactions:3 interactions with chain D- Hydrophobic interactions: D:A.197
- Hydrogen bonds: D:D.276
- pi-Stacking: D:H.194
BPY.26: 7 residues within 4Å:- Chain D: A.22, S.25, F.26, M.30, I.238, T.259, P.260
4 PLIP interactions:4 interactions with chain D- Hydrophobic interactions: D:F.26, D:I.238, D:I.238, D:P.260
BPY.31: 14 residues within 4Å:- Chain E: H.152, I.154, L.190, F.192, H.200, H.215, H.247, N.249, D.250, Y.256, E.266, L.297
- Ligands: FE2.30, GOL.35
9 PLIP interactions:9 interactions with chain E- Hydrophobic interactions: E:I.154, E:L.190, E:F.192, E:F.192, E:H.247, E:L.297
- Hydrogen bonds: E:Y.256
- pi-Stacking: E:H.247
- pi-Cation interactions: E:H.215
BPY.32: 7 residues within 4Å:- Chain E: G.171, R.173, H.194, C.195, N.196, A.197, D.276
3 PLIP interactions:3 interactions with chain E- Hydrophobic interactions: E:A.197
- Hydrogen bonds: E:D.276
- pi-Stacking: E:H.194
BPY.33: 7 residues within 4Å:- Chain E: A.22, S.25, F.26, M.30, I.238, T.259, P.260
4 PLIP interactions:4 interactions with chain E- Hydrophobic interactions: E:F.26, E:I.238, E:I.238, E:P.260
BPY.38: 14 residues within 4Å:- Chain F: H.152, I.154, L.190, F.192, H.200, H.215, H.247, N.249, D.250, Y.256, E.266, L.297
- Ligands: FE2.37, GOL.42
9 PLIP interactions:9 interactions with chain F- Hydrophobic interactions: F:I.154, F:L.190, F:F.192, F:F.192, F:H.247, F:L.297
- Hydrogen bonds: F:Y.256
- pi-Stacking: F:H.247
- pi-Cation interactions: F:H.215
BPY.39: 7 residues within 4Å:- Chain F: G.171, R.173, H.194, C.195, N.196, A.197, D.276
3 PLIP interactions:3 interactions with chain F- Hydrophobic interactions: F:A.197
- Hydrogen bonds: F:D.276
- pi-Stacking: F:H.194
BPY.40: 7 residues within 4Å:- Chain F: A.22, S.25, F.26, M.30, I.238, T.259, P.260
4 PLIP interactions:4 interactions with chain F- Hydrophobic interactions: F:F.26, F:I.238, F:I.238, F:P.260
BPY.45: 14 residues within 4Å:- Chain G: H.152, I.154, L.190, F.192, H.200, H.215, H.247, N.249, D.250, Y.256, E.266, L.297
- Ligands: FE2.44, GOL.49
9 PLIP interactions:9 interactions with chain G- Hydrophobic interactions: G:I.154, G:L.190, G:F.192, G:F.192, G:H.247, G:L.297
- Hydrogen bonds: G:Y.256
- pi-Stacking: G:H.247
- pi-Cation interactions: G:H.215
BPY.46: 7 residues within 4Å:- Chain G: G.171, R.173, H.194, C.195, N.196, A.197, D.276
3 PLIP interactions:3 interactions with chain G- Hydrophobic interactions: G:A.197
- Hydrogen bonds: G:D.276
- pi-Stacking: G:H.194
BPY.47: 7 residues within 4Å:- Chain G: A.22, S.25, F.26, M.30, I.238, T.259, P.260
4 PLIP interactions:4 interactions with chain G- Hydrophobic interactions: G:F.26, G:I.238, G:I.238, G:P.260
BPY.52: 14 residues within 4Å:- Chain H: H.152, I.154, L.190, F.192, H.200, H.215, H.247, N.249, D.250, Y.256, E.266, L.297
- Ligands: FE2.51, GOL.56
9 PLIP interactions:9 interactions with chain H- Hydrophobic interactions: H:I.154, H:L.190, H:F.192, H:F.192, H:H.247, H:L.297
- Hydrogen bonds: H:Y.256
- pi-Stacking: H:H.247
- pi-Cation interactions: H:H.215
BPY.53: 7 residues within 4Å:- Chain H: G.171, R.173, H.194, C.195, N.196, A.197, D.276
3 PLIP interactions:3 interactions with chain H- Hydrophobic interactions: H:A.197
- Hydrogen bonds: H:D.276
- pi-Stacking: H:H.194
BPY.54: 7 residues within 4Å:- Chain H: A.22, S.25, F.26, M.30, I.238, T.259, P.260
4 PLIP interactions:4 interactions with chain H- Hydrophobic interactions: H:F.26, H:I.238, H:I.238, H:P.260
- 16 x GOL: GLYCEROL(Non-functional Binders)
GOL.6: 9 residues within 4Å:- Chain A: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126
Ligand excluded by PLIPGOL.7: 8 residues within 4Å:- Chain A: Y.178, L.190, F.192, H.247, Y.256, L.301
- Ligands: FE2.2, BPY.3
Ligand excluded by PLIPGOL.13: 9 residues within 4Å:- Chain B: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126
Ligand excluded by PLIPGOL.14: 8 residues within 4Å:- Chain B: Y.178, L.190, F.192, H.247, Y.256, L.301
- Ligands: FE2.9, BPY.10
Ligand excluded by PLIPGOL.20: 9 residues within 4Å:- Chain C: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126
Ligand excluded by PLIPGOL.21: 8 residues within 4Å:- Chain C: Y.178, L.190, F.192, H.247, Y.256, L.301
- Ligands: FE2.16, BPY.17
Ligand excluded by PLIPGOL.27: 9 residues within 4Å:- Chain D: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126
Ligand excluded by PLIPGOL.28: 8 residues within 4Å:- Chain D: Y.178, L.190, F.192, H.247, Y.256, L.301
- Ligands: FE2.23, BPY.24
Ligand excluded by PLIPGOL.34: 9 residues within 4Å:- Chain E: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126
Ligand excluded by PLIPGOL.35: 8 residues within 4Å:- Chain E: Y.178, L.190, F.192, H.247, Y.256, L.301
- Ligands: FE2.30, BPY.31
Ligand excluded by PLIPGOL.41: 9 residues within 4Å:- Chain F: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126
Ligand excluded by PLIPGOL.42: 8 residues within 4Å:- Chain F: Y.178, L.190, F.192, H.247, Y.256, L.301
- Ligands: FE2.37, BPY.38
Ligand excluded by PLIPGOL.48: 9 residues within 4Å:- Chain G: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126
Ligand excluded by PLIPGOL.49: 8 residues within 4Å:- Chain G: Y.178, L.190, F.192, H.247, Y.256, L.301
- Ligands: FE2.44, BPY.45
Ligand excluded by PLIPGOL.55: 9 residues within 4Å:- Chain H: Y.12, W.51, H.52, H.53, R.103, M.104, V.105, P.125, R.126
Ligand excluded by PLIPGOL.56: 8 residues within 4Å:- Chain H: Y.178, L.190, F.192, H.247, Y.256, L.301
- Ligands: FE2.51, BPY.52
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Neau, D.B. et al., Structural explanation for success and failure in the enzymatic ring-cleavage of 3,4 dihydroxybiphenyl and related PCB metabolites. To be Published
- Release Date
- 2008-02-19
- Peptides
- 1,2-dihydroxynaphthalene dioxygenase: ABCDEFGH
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
AE
AF
AG
AH
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-octamer
- Ligands
- 8 x MG: MAGNESIUM ION(Non-covalent)
- 8 x FE2: FE (II) ION(Non-covalent)
- 24 x BPY: BIPHENYL-2,3-DIOL(Non-covalent)
- 16 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Neau, D.B. et al., Structural explanation for success and failure in the enzymatic ring-cleavage of 3,4 dihydroxybiphenyl and related PCB metabolites. To be Published
- Release Date
- 2008-02-19
- Peptides
- 1,2-dihydroxynaphthalene dioxygenase: ABCDEFGH
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
AE
AF
AG
AH
A