- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- hetero-3-3-mer
- Ligands
- 3 x FE: FE (III) ION(Non-covalent)
- 12 x SO4: SULFATE ION(Non-functional Binders)
SO4.2: 3 residues within 4Å:- Chain A: K.245, W.439, H.440
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:W.439
- Salt bridges: A:K.245
SO4.3: 4 residues within 4Å:- Chain A: L.128, N.129, K.130, K.131
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:K.130, A:K.131
- Water bridges: A:E.120, A:L.128
- Salt bridges: A:K.130
SO4.20: 2 residues within 4Å:- Chain B: Q.63, Q.65
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:Q.63, B:Q.63, B:Q.65
- Water bridges: B:N.89
SO4.21: 7 residues within 4Å:- Chain B: G.59, S.60, E.61, G.166, E.167, K.172
- Ligands: EDO.29
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:S.60, B:E.167, B:E.167
- Water bridges: B:K.172
- Salt bridges: B:K.172
SO4.32: 3 residues within 4Å:- Chain C: K.245, W.439, H.440
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:W.439
- Salt bridges: C:K.245
SO4.33: 4 residues within 4Å:- Chain C: L.128, N.129, K.130, K.131
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:K.130, C:K.131
- Water bridges: C:E.120, C:L.128
- Salt bridges: C:K.130
SO4.50: 2 residues within 4Å:- Chain D: Q.63, Q.65
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:Q.63, D:Q.63, D:Q.65
- Water bridges: D:N.89
SO4.51: 7 residues within 4Å:- Chain D: G.59, S.60, E.61, G.166, E.167, K.172
- Ligands: EDO.59
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:S.60, D:E.167, D:E.167
- Water bridges: D:K.172
- Salt bridges: D:K.172
SO4.62: 3 residues within 4Å:- Chain E: K.245, W.439, H.440
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:W.439
- Salt bridges: E:K.245
SO4.63: 4 residues within 4Å:- Chain E: L.128, N.129, K.130, K.131
5 PLIP interactions:5 interactions with chain E- Hydrogen bonds: E:K.130, E:K.131
- Water bridges: E:E.120, E:L.128
- Salt bridges: E:K.130
SO4.80: 2 residues within 4Å:- Chain F: Q.63, Q.65
4 PLIP interactions:4 interactions with chain F- Hydrogen bonds: F:Q.63, F:Q.63, F:Q.65
- Water bridges: F:N.89
SO4.81: 7 residues within 4Å:- Chain F: G.59, S.60, E.61, G.166, E.167, K.172
- Ligands: EDO.89
5 PLIP interactions:5 interactions with chain F- Hydrogen bonds: F:S.60, F:E.167, F:E.167
- Water bridges: F:K.172
- Salt bridges: F:K.172
- 3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
FES.4: 10 residues within 4Å:- Chain A: C.81, H.83, R.84, G.85, K.86, C.101, Y.103, H.104, G.105, W.106
4 PLIP interactions:4 interactions with chain A,- Metal complexes: A:C.81, A:H.83, A:C.101, A:H.104
FES.34: 10 residues within 4Å:- Chain C: C.81, H.83, R.84, G.85, K.86, C.101, Y.103, H.104, G.105, W.106
4 PLIP interactions:4 interactions with chain C,- Metal complexes: C:C.81, C:H.83, C:C.101, C:H.104
FES.64: 10 residues within 4Å:- Chain E: C.81, H.83, R.84, G.85, K.86, C.101, Y.103, H.104, G.105, W.106
4 PLIP interactions:4 interactions with chain E,- Metal complexes: E:C.81, E:H.83, E:C.101, E:H.104
- 3 x AN3: ANTHRACENE(Non-covalent)
AN3.5: 12 residues within 4Å:- Chain A: N.201, F.202, D.205, H.208, V.209, F.224, L.253, V.260, H.295, N.297, L.307, W.358
9 PLIP interactions:9 interactions with chain A- Hydrophobic interactions: A:V.209, A:F.224, A:L.253, A:V.260, A:N.297, A:L.307, A:W.358
- pi-Stacking: A:H.208
- pi-Cation interactions: A:H.295
AN3.35: 12 residues within 4Å:- Chain C: N.201, F.202, D.205, H.208, V.209, F.224, L.253, V.260, H.295, N.297, L.307, W.358
9 PLIP interactions:9 interactions with chain C- Hydrophobic interactions: C:V.209, C:F.224, C:L.253, C:V.260, C:N.297, C:L.307, C:W.358
- pi-Stacking: C:H.208
- pi-Cation interactions: C:H.295
AN3.65: 12 residues within 4Å:- Chain E: N.201, F.202, D.205, H.208, V.209, F.224, L.253, V.260, H.295, N.297, L.307, W.358
9 PLIP interactions:9 interactions with chain E- Hydrophobic interactions: E:V.209, E:F.224, E:L.253, E:V.260, E:N.297, E:L.307, E:W.358
- pi-Stacking: E:H.208
- pi-Cation interactions: E:H.295
- 69 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.6: 7 residues within 4Å:- Chain A: P.49, A.50, D.53
- Chain B: R.78, Y.79, K.80, L.81
Ligand excluded by PLIPEDO.7: 2 residues within 4Å:- Chain A: P.118, F.119
Ligand excluded by PLIPEDO.8: 8 residues within 4Å:- Chain A: T.56, E.92, P.186, K.188, W.327, Y.329
- Chain B: E.70, R.183
Ligand excluded by PLIPEDO.9: 7 residues within 4Å:- Chain A: V.183, R.342, A.345, D.346
- Chain B: N.82, N.86
- Ligands: EDO.30
Ligand excluded by PLIPEDO.10: 2 residues within 4Å:- Chain A: E.24, K.374
Ligand excluded by PLIPEDO.11: 4 residues within 4Å:- Chain A: Y.376, Q.377, D.380
- Chain E: K.136
Ligand excluded by PLIPEDO.12: 5 residues within 4Å:- Chain A: S.73, I.74, V.141, E.142, S.143
Ligand excluded by PLIPEDO.13: 5 residues within 4Å:- Chain A: G.239, L.240, W.254, Y.399, K.405
Ligand excluded by PLIPEDO.14: 6 residues within 4Å:- Chain A: H.176, S.177, K.276, R.279, L.280, D.335
Ligand excluded by PLIPEDO.15: 7 residues within 4Å:- Chain A: N.4, H.29, T.33, V.424, S.425, S.426
- Ligands: EDO.16
Ligand excluded by PLIPEDO.16: 3 residues within 4Å:- Chain A: H.29, K.32
- Ligands: EDO.15
Ligand excluded by PLIPEDO.17: 6 residues within 4Å:- Chain A: G.98, F.99, V.100, G.107, F.108, Q.115
Ligand excluded by PLIPEDO.18: 10 residues within 4Å:- Chain A: L.31, F.35, A.36, M.59, G.60, I.61, D.62, F.152
- Chain C: Y.376, Q.377
Ligand excluded by PLIPEDO.19: 7 residues within 4Å:- Chain A: H.18, S.381, D.382, L.383
- Chain E: V.80, C.81, R.82
Ligand excluded by PLIPEDO.22: 6 residues within 4Å:- Chain B: Y.50, Y.88, Q.102, M.191, V.192, F.193
Ligand excluded by PLIPEDO.23: 2 residues within 4Å:- Chain B: N.91, Q.94
Ligand excluded by PLIPEDO.24: 7 residues within 4Å:- Chain B: R.138, A.158, E.160, F.177, V.178, D.179
- Ligands: EDO.58
Ligand excluded by PLIPEDO.25: 3 residues within 4Å:- Chain B: E.83, A.84, N.86
Ligand excluded by PLIPEDO.26: 2 residues within 4Å:- Chain A: T.368
- Chain B: R.148
Ligand excluded by PLIPEDO.27: 5 residues within 4Å:- Chain A: V.190, K.192
- Chain B: Q.186, T.187, H.188
Ligand excluded by PLIPEDO.28: 5 residues within 4Å:- Chain B: D.46, R.115, F.116
- Chain F: R.138
- Ligands: EDO.84
Ligand excluded by PLIPEDO.29: 9 residues within 4Å:- Chain B: G.59, S.60, E.61, K.164, R.165, G.166, K.172, V.174
- Ligands: SO4.21
Ligand excluded by PLIPEDO.30: 4 residues within 4Å:- Chain A: V.183, R.342
- Chain B: N.82
- Ligands: EDO.9
Ligand excluded by PLIPEDO.36: 7 residues within 4Å:- Chain C: P.49, A.50, D.53
- Chain D: R.78, Y.79, K.80, L.81
Ligand excluded by PLIPEDO.37: 2 residues within 4Å:- Chain C: P.118, F.119
Ligand excluded by PLIPEDO.38: 8 residues within 4Å:- Chain C: T.56, E.92, P.186, K.188, W.327, Y.329
- Chain D: E.70, R.183
Ligand excluded by PLIPEDO.39: 7 residues within 4Å:- Chain C: V.183, R.342, A.345, D.346
- Chain D: N.82, N.86
- Ligands: EDO.60
Ligand excluded by PLIPEDO.40: 2 residues within 4Å:- Chain C: E.24, K.374
Ligand excluded by PLIPEDO.41: 4 residues within 4Å:- Chain A: K.136
- Chain C: Y.376, Q.377, D.380
Ligand excluded by PLIPEDO.42: 5 residues within 4Å:- Chain C: S.73, I.74, V.141, E.142, S.143
Ligand excluded by PLIPEDO.43: 5 residues within 4Å:- Chain C: G.239, L.240, W.254, Y.399, K.405
Ligand excluded by PLIPEDO.44: 6 residues within 4Å:- Chain C: H.176, S.177, K.276, R.279, L.280, D.335
Ligand excluded by PLIPEDO.45: 7 residues within 4Å:- Chain C: N.4, H.29, T.33, V.424, S.425, S.426
- Ligands: EDO.46
Ligand excluded by PLIPEDO.46: 3 residues within 4Å:- Chain C: H.29, K.32
- Ligands: EDO.45
Ligand excluded by PLIPEDO.47: 6 residues within 4Å:- Chain C: G.98, F.99, V.100, G.107, F.108, Q.115
Ligand excluded by PLIPEDO.48: 10 residues within 4Å:- Chain C: L.31, F.35, A.36, M.59, G.60, I.61, D.62, F.152
- Chain E: Y.376, Q.377
Ligand excluded by PLIPEDO.49: 7 residues within 4Å:- Chain A: V.80, C.81, R.82
- Chain C: H.18, S.381, D.382, L.383
Ligand excluded by PLIPEDO.52: 6 residues within 4Å:- Chain D: Y.50, Y.88, Q.102, M.191, V.192, F.193
Ligand excluded by PLIPEDO.53: 2 residues within 4Å:- Chain D: N.91, Q.94
Ligand excluded by PLIPEDO.54: 7 residues within 4Å:- Chain D: R.138, A.158, E.160, F.177, V.178, D.179
- Ligands: EDO.88
Ligand excluded by PLIPEDO.55: 3 residues within 4Å:- Chain D: E.83, A.84, N.86
Ligand excluded by PLIPEDO.56: 2 residues within 4Å:- Chain C: T.368
- Chain D: R.148
Ligand excluded by PLIPEDO.57: 5 residues within 4Å:- Chain C: V.190, K.192
- Chain D: Q.186, T.187, H.188
Ligand excluded by PLIPEDO.58: 5 residues within 4Å:- Chain B: R.138
- Chain D: D.46, R.115, F.116
- Ligands: EDO.24
Ligand excluded by PLIPEDO.59: 9 residues within 4Å:- Chain D: G.59, S.60, E.61, K.164, R.165, G.166, K.172, V.174
- Ligands: SO4.51
Ligand excluded by PLIPEDO.60: 4 residues within 4Å:- Chain C: V.183, R.342
- Chain D: N.82
- Ligands: EDO.39
Ligand excluded by PLIPEDO.66: 7 residues within 4Å:- Chain E: P.49, A.50, D.53
- Chain F: R.78, Y.79, K.80, L.81
Ligand excluded by PLIPEDO.67: 2 residues within 4Å:- Chain E: P.118, F.119
Ligand excluded by PLIPEDO.68: 8 residues within 4Å:- Chain E: T.56, E.92, P.186, K.188, W.327, Y.329
- Chain F: E.70, R.183
Ligand excluded by PLIPEDO.69: 7 residues within 4Å:- Chain E: V.183, R.342, A.345, D.346
- Chain F: N.82, N.86
- Ligands: EDO.90
Ligand excluded by PLIPEDO.70: 2 residues within 4Å:- Chain E: E.24, K.374
Ligand excluded by PLIPEDO.71: 4 residues within 4Å:- Chain C: K.136
- Chain E: Y.376, Q.377, D.380
Ligand excluded by PLIPEDO.72: 5 residues within 4Å:- Chain E: S.73, I.74, V.141, E.142, S.143
Ligand excluded by PLIPEDO.73: 5 residues within 4Å:- Chain E: G.239, L.240, W.254, Y.399, K.405
Ligand excluded by PLIPEDO.74: 6 residues within 4Å:- Chain E: H.176, S.177, K.276, R.279, L.280, D.335
Ligand excluded by PLIPEDO.75: 7 residues within 4Å:- Chain E: N.4, H.29, T.33, V.424, S.425, S.426
- Ligands: EDO.76
Ligand excluded by PLIPEDO.76: 3 residues within 4Å:- Chain E: H.29, K.32
- Ligands: EDO.75
Ligand excluded by PLIPEDO.77: 6 residues within 4Å:- Chain E: G.98, F.99, V.100, G.107, F.108, Q.115
Ligand excluded by PLIPEDO.78: 10 residues within 4Å:- Chain A: Y.376, Q.377
- Chain E: L.31, F.35, A.36, M.59, G.60, I.61, D.62, F.152
Ligand excluded by PLIPEDO.79: 7 residues within 4Å:- Chain C: V.80, C.81, R.82
- Chain E: H.18, S.381, D.382, L.383
Ligand excluded by PLIPEDO.82: 6 residues within 4Å:- Chain F: Y.50, Y.88, Q.102, M.191, V.192, F.193
Ligand excluded by PLIPEDO.83: 2 residues within 4Å:- Chain F: N.91, Q.94
Ligand excluded by PLIPEDO.84: 7 residues within 4Å:- Chain F: R.138, A.158, E.160, F.177, V.178, D.179
- Ligands: EDO.28
Ligand excluded by PLIPEDO.85: 3 residues within 4Å:- Chain F: E.83, A.84, N.86
Ligand excluded by PLIPEDO.86: 2 residues within 4Å:- Chain E: T.368
- Chain F: R.148
Ligand excluded by PLIPEDO.87: 5 residues within 4Å:- Chain E: V.190, K.192
- Chain F: Q.186, T.187, H.188
Ligand excluded by PLIPEDO.88: 5 residues within 4Å:- Chain D: R.138
- Chain F: D.46, R.115, F.116
- Ligands: EDO.54
Ligand excluded by PLIPEDO.89: 9 residues within 4Å:- Chain F: G.59, S.60, E.61, K.164, R.165, G.166, K.172, V.174
- Ligands: SO4.81
Ligand excluded by PLIPEDO.90: 4 residues within 4Å:- Chain E: V.183, R.342
- Chain F: N.82
- Ligands: EDO.69
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ferraro, D.J. et al., Structural basis for regioselectivity and stereoselectivity of product formation by naphthalene 1,2-dioxygenase. J.Bacteriol. (2006)
- Release Date
- 2006-10-10
- Peptides
- Naphthalene 1,2-dioxygenase alpha subunit: ACE
Naphthalene 1,2-dioxygenase beta subunit: BDF - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
AE
AB
BD
BF
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- hetero-3-3-mer
- Ligands
- 3 x FE: FE (III) ION(Non-covalent)
- 12 x SO4: SULFATE ION(Non-functional Binders)
- 3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 3 x AN3: ANTHRACENE(Non-covalent)
- 69 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ferraro, D.J. et al., Structural basis for regioselectivity and stereoselectivity of product formation by naphthalene 1,2-dioxygenase. J.Bacteriol. (2006)
- Release Date
- 2006-10-10
- Peptides
- Naphthalene 1,2-dioxygenase alpha subunit: ACE
Naphthalene 1,2-dioxygenase beta subunit: BDF - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
AE
AB
BD
BF
B