- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.65 Å
- Oligo State
- hetero-3-3-mer
- Ligands
- 3 x FE: FE (III) ION(Non-covalent)
- 15 x SO4: SULFATE ION(Non-functional Binders)
SO4.2: 4 residues within 4Å:- Chain A: K.245, W.439, H.440
- Ligands: EDO.12
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
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.130, A:K.131
- Salt bridges: A:K.130
SO4.20: 2 residues within 4Å:- Chain B: Q.63, Q.65
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:Q.63, B:Q.65
- Water bridges: B:Q.65
SO4.21: 5 residues within 4Å:- Chain B: G.59, S.60, G.166, E.167, K.172
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:S.60, B:E.167
- Water bridges: B:E.61, B:K.172
- Salt bridges: B:K.172
SO4.22: 5 residues within 4Å:- Chain A: T.368
- Chain B: R.148
- Chain E: T.87, V.89, S.90
7 PLIP interactions:3 interactions with chain E, 4 interactions with chain B- Hydrogen bonds: E:V.89
- Water bridges: E:N.79, E:T.87, B:R.148, B:R.148, B:R.148
- Salt bridges: B:R.148
SO4.30: 4 residues within 4Å:- Chain C: K.245, W.439, H.440
- Ligands: EDO.40
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:W.439
- Salt bridges: C:K.245
SO4.31: 4 residues within 4Å:- Chain C: L.128, N.129, K.130, K.131
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:K.130, C:K.131
- Salt bridges: C:K.130
SO4.48: 2 residues within 4Å:- Chain D: Q.63, Q.65
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:Q.63, D:Q.65
- Water bridges: D:Q.65
SO4.49: 5 residues within 4Å:- Chain D: G.59, S.60, G.166, E.167, K.172
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:S.60, D:E.167
- Water bridges: D:E.61, D:K.172
- Salt bridges: D:K.172
SO4.50: 5 residues within 4Å:- Chain A: T.87, V.89, S.90
- Chain C: T.368
- Chain D: R.148
7 PLIP interactions:3 interactions with chain A, 4 interactions with chain D- Hydrogen bonds: A:V.89
- Water bridges: A:N.79, A:T.87, D:R.148, D:R.148, D:R.148
- Salt bridges: D:R.148
SO4.58: 4 residues within 4Å:- Chain E: K.245, W.439, H.440
- Ligands: EDO.68
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:W.439
- Salt bridges: E:K.245
SO4.59: 4 residues within 4Å:- Chain E: L.128, N.129, K.130, K.131
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:K.130, E:K.131
- Salt bridges: E:K.130
SO4.76: 2 residues within 4Å:- Chain F: Q.63, Q.65
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:Q.63, F:Q.65
- Water bridges: F:Q.65
SO4.77: 5 residues within 4Å:- Chain F: G.59, S.60, G.166, E.167, K.172
5 PLIP interactions:5 interactions with chain F- Hydrogen bonds: F:S.60, F:E.167
- Water bridges: F:E.61, F:K.172
- Salt bridges: F:K.172
SO4.78: 5 residues within 4Å:- Chain C: T.87, V.89, S.90
- Chain E: T.368
- Chain F: R.148
7 PLIP interactions:3 interactions with chain C, 4 interactions with chain F- Hydrogen bonds: C:V.89
- Water bridges: C:N.79, C:T.87, F:R.148, F:R.148, F:R.148
- Salt bridges: F:R.148
- 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.32: 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.60: 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 PEY: PHENANTHRENE(Non-covalent)
PEY.5: 9 residues within 4Å:- Chain A: N.201, D.205, H.208, V.209, F.224, V.260, H.295, N.297, L.307
7 PLIP interactions:7 interactions with chain A- Hydrophobic interactions: A:V.209, A:F.224, A:V.260, A:N.297, A:L.307
- pi-Stacking: A:H.208
- pi-Cation interactions: A:H.295
PEY.33: 9 residues within 4Å:- Chain C: N.201, D.205, H.208, V.209, F.224, V.260, H.295, N.297, L.307
7 PLIP interactions:7 interactions with chain C- Hydrophobic interactions: C:V.209, C:F.224, C:V.260, C:N.297, C:L.307
- pi-Stacking: C:H.208
- pi-Cation interactions: C:H.295
PEY.61: 9 residues within 4Å:- Chain E: N.201, D.205, H.208, V.209, F.224, V.260, H.295, N.297, L.307
7 PLIP interactions:7 interactions with chain E- Hydrophobic interactions: E:V.209, E:F.224, E:V.260, E:N.297, E:L.307
- pi-Stacking: E:H.208
- pi-Cation interactions: E:H.295
- 60 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.6: 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.7: 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.8: 3 residues within 4Å:- Chain A: E.24, K.374
- Ligands: EDO.9
Ligand excluded by PLIPEDO.9: 5 residues within 4Å:- Chain A: G.22, K.374, R.379
- Chain E: Q.28
- Ligands: EDO.8
Ligand excluded by PLIPEDO.10: 2 residues within 4Å:- Chain A: P.118, F.119
Ligand excluded by PLIPEDO.11: 5 residues within 4Å:- Chain A: V.183, R.342, A.345, D.346
- Chain B: N.82
Ligand excluded by PLIPEDO.12: 1 residues within 4Å:- Ligands: SO4.2
Ligand excluded by PLIPEDO.13: 5 residues within 4Å:- Chain A: W.168, D.396, A.397, V.398, P.400
Ligand excluded by PLIPEDO.14: 3 residues within 4Å:- Chain A: W.254, R.290, Y.399
Ligand excluded by PLIPEDO.15: 8 residues within 4Å:- Chain A: V.55, T.56, E.92, P.186, K.188, W.327
- Chain B: E.70, R.183
Ligand excluded by PLIPEDO.16: 4 residues within 4Å:- Chain A: F.272, A.275, K.276, R.279
Ligand excluded by PLIPEDO.17: 6 residues within 4Å:- Chain A: H.176, S.177, K.276, R.279, L.280, D.335
Ligand excluded by PLIPEDO.18: 8 residues within 4Å:- Chain A: Y.3, N.4, H.29, T.33, V.424, S.425, S.426, S.427
Ligand excluded by PLIPEDO.19: 3 residues within 4Å:- Chain A: K.136
- Chain C: Q.377, D.380
Ligand excluded by PLIPEDO.23: 4 residues within 4Å:- Chain B: D.46, R.115, F.116
- Ligands: EDO.83
Ligand excluded by PLIPEDO.24: 3 residues within 4Å:- Chain B: E.83, A.84, N.86
Ligand excluded by PLIPEDO.25: 6 residues within 4Å:- Chain B: Y.50, Y.88, Q.102, M.191, V.192, F.193
Ligand excluded by PLIPEDO.26: 2 residues within 4Å:- Chain B: N.91, Q.94
Ligand excluded by PLIPEDO.27: 7 residues within 4Å:- Chain B: R.138, A.158, E.160, F.177, V.178, D.179
- Ligands: EDO.51
Ligand excluded by PLIPEDO.28: 5 residues within 4Å:- Chain A: V.190, K.192
- Chain B: Q.186, T.187, H.188
Ligand excluded by PLIPEDO.34: 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.35: 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.36: 3 residues within 4Å:- Chain C: E.24, K.374
- Ligands: EDO.37
Ligand excluded by PLIPEDO.37: 5 residues within 4Å:- Chain A: Q.28
- Chain C: G.22, K.374, R.379
- Ligands: EDO.36
Ligand excluded by PLIPEDO.38: 2 residues within 4Å:- Chain C: P.118, F.119
Ligand excluded by PLIPEDO.39: 5 residues within 4Å:- Chain C: V.183, R.342, A.345, D.346
- Chain D: N.82
Ligand excluded by PLIPEDO.40: 1 residues within 4Å:- Ligands: SO4.30
Ligand excluded by PLIPEDO.41: 5 residues within 4Å:- Chain C: W.168, D.396, A.397, V.398, P.400
Ligand excluded by PLIPEDO.42: 3 residues within 4Å:- Chain C: W.254, R.290, Y.399
Ligand excluded by PLIPEDO.43: 8 residues within 4Å:- Chain C: V.55, T.56, E.92, P.186, K.188, W.327
- Chain D: E.70, R.183
Ligand excluded by PLIPEDO.44: 4 residues within 4Å:- Chain C: F.272, A.275, K.276, R.279
Ligand excluded by PLIPEDO.45: 6 residues within 4Å:- Chain C: H.176, S.177, K.276, R.279, L.280, D.335
Ligand excluded by PLIPEDO.46: 8 residues within 4Å:- Chain C: Y.3, N.4, H.29, T.33, V.424, S.425, S.426, S.427
Ligand excluded by PLIPEDO.47: 3 residues within 4Å:- Chain C: K.136
- Chain E: Q.377, D.380
Ligand excluded by PLIPEDO.51: 4 residues within 4Å:- Chain D: D.46, R.115, F.116
- Ligands: EDO.27
Ligand excluded by PLIPEDO.52: 3 residues within 4Å:- Chain D: E.83, A.84, N.86
Ligand excluded by PLIPEDO.53: 6 residues within 4Å:- Chain D: Y.50, Y.88, Q.102, M.191, V.192, F.193
Ligand excluded by PLIPEDO.54: 2 residues within 4Å:- Chain D: N.91, Q.94
Ligand excluded by PLIPEDO.55: 7 residues within 4Å:- Chain D: R.138, A.158, E.160, F.177, V.178, D.179
- Ligands: EDO.79
Ligand excluded by PLIPEDO.56: 5 residues within 4Å:- Chain C: V.190, K.192
- Chain D: Q.186, T.187, H.188
Ligand excluded by PLIPEDO.62: 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.63: 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.64: 3 residues within 4Å:- Chain E: E.24, K.374
- Ligands: EDO.65
Ligand excluded by PLIPEDO.65: 5 residues within 4Å:- Chain C: Q.28
- Chain E: G.22, K.374, R.379
- Ligands: EDO.64
Ligand excluded by PLIPEDO.66: 2 residues within 4Å:- Chain E: P.118, F.119
Ligand excluded by PLIPEDO.67: 5 residues within 4Å:- Chain E: V.183, R.342, A.345, D.346
- Chain F: N.82
Ligand excluded by PLIPEDO.68: 1 residues within 4Å:- Ligands: SO4.58
Ligand excluded by PLIPEDO.69: 5 residues within 4Å:- Chain E: W.168, D.396, A.397, V.398, P.400
Ligand excluded by PLIPEDO.70: 3 residues within 4Å:- Chain E: W.254, R.290, Y.399
Ligand excluded by PLIPEDO.71: 8 residues within 4Å:- Chain E: V.55, T.56, E.92, P.186, K.188, W.327
- Chain F: E.70, R.183
Ligand excluded by PLIPEDO.72: 4 residues within 4Å:- Chain E: F.272, A.275, K.276, R.279
Ligand excluded by PLIPEDO.73: 6 residues within 4Å:- Chain E: H.176, S.177, K.276, R.279, L.280, D.335
Ligand excluded by PLIPEDO.74: 8 residues within 4Å:- Chain E: Y.3, N.4, H.29, T.33, V.424, S.425, S.426, S.427
Ligand excluded by PLIPEDO.75: 3 residues within 4Å:- Chain A: Q.377, D.380
- Chain E: K.136
Ligand excluded by PLIPEDO.79: 4 residues within 4Å:- Chain F: D.46, R.115, F.116
- Ligands: EDO.55
Ligand excluded by PLIPEDO.80: 3 residues within 4Å:- Chain F: E.83, A.84, N.86
Ligand excluded by PLIPEDO.81: 6 residues within 4Å:- Chain F: Y.50, Y.88, Q.102, M.191, V.192, F.193
Ligand excluded by PLIPEDO.82: 2 residues within 4Å:- Chain F: N.91, Q.94
Ligand excluded by PLIPEDO.83: 7 residues within 4Å:- Chain F: R.138, A.158, E.160, F.177, V.178, D.179
- Ligands: EDO.23
Ligand excluded by PLIPEDO.84: 5 residues within 4Å:- Chain E: V.190, K.192
- Chain F: Q.186, T.187, H.188
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 1.65 Å
- Oligo State
- hetero-3-3-mer
- Ligands
- 3 x FE: FE (III) ION(Non-covalent)
- 15 x SO4: SULFATE ION(Non-functional Binders)
- 3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 3 x PEY: PHENANTHRENE(Non-covalent)
- 60 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