- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.50 Å
- Oligo State
- hetero-3-3-mer
- Ligands
- 24 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 12 x SO4: SULFATE ION(Non-functional Binders)
SO4.3: 4 residues within 4Å:- Chain A: L.128, N.129, K.130, K.131
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:K.130, A:K.131
- Water bridges: A:E.120, A:E.126, A:L.128, A:K.130
- Salt bridges: A:K.130
SO4.9: 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
SO4.13: 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
SO4.14: 6 residues within 4Å:- Chain B: G.59, S.60, E.61, G.166, E.167, K.172
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:S.60, B:E.167, B:E.167, B:E.167
- Water bridges: B:K.172
- Salt bridges: B:K.172
SO4.18: 4 residues within 4Å:- Chain C: L.128, N.129, K.130, K.131
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:K.130, C:K.131
- Water bridges: C:E.120, C:E.126, C:L.128, C:K.130
- Salt bridges: C:K.130
SO4.24: 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
SO4.28: 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
SO4.29: 6 residues within 4Å:- Chain D: G.59, S.60, E.61, G.166, E.167, K.172
6 PLIP interactions:6 interactions with chain D- Hydrogen bonds: D:S.60, D:E.167, D:E.167, D:E.167
- Water bridges: D:K.172
- Salt bridges: D:K.172
SO4.33: 4 residues within 4Å:- Chain E: L.128, N.129, K.130, K.131
7 PLIP interactions:7 interactions with chain E- Hydrogen bonds: E:K.130, E:K.131
- Water bridges: E:E.120, E:E.126, E:L.128, E:K.130
- Salt bridges: E:K.130
SO4.39: 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
SO4.43: 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
SO4.44: 6 residues within 4Å:- Chain F: G.59, S.60, E.61, G.166, E.167, K.172
6 PLIP interactions:6 interactions with chain F- Hydrogen bonds: F:S.60, F:E.167, 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.19: 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.34: 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 FE: FE (III) ION(Non-covalent)
FE.5: 4 residues within 4Å:- Chain A: N.201, H.208, H.213, D.362
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:H.208, A:H.213, A:D.362, A:D.362, H2O.18
FE.20: 4 residues within 4Å:- Chain C: N.201, H.208, H.213, D.362
5 PLIP interactions:4 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:H.208, C:H.213, C:D.362, C:D.362, H2O.41
FE.35: 4 residues within 4Å:- Chain E: N.201, H.208, H.213, D.362
5 PLIP interactions:4 interactions with chain E, 1 Ligand-Water interactions- Metal complexes: E:H.208, E:H.213, E:D.362, E:D.362, H2O.65
- 3 x 16N: 2,3-dihydro-1H-indene(Non-covalent)
16N.6: 7 residues within 4Å:- Chain A: N.201, D.205, H.208, V.209, H.295, N.297, L.307
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:V.209, A:N.297, A:L.307
- pi-Stacking: A:H.208
16N.21: 7 residues within 4Å:- Chain C: N.201, D.205, H.208, V.209, H.295, N.297, L.307
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:V.209, C:N.297, C:L.307
- pi-Stacking: C:H.208
16N.36: 7 residues within 4Å:- Chain E: N.201, D.205, H.208, V.209, H.295, N.297, L.307
4 PLIP interactions:4 interactions with chain E- Hydrophobic interactions: E:V.209, E:N.297, E:L.307
- pi-Stacking: E:H.208
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ferraro, D.J. et al., One enzyme, many reactions: structural basis for the various reactions catalyzed by naphthalene 1,2-dioxygenase. Iucrj (2017)
- Release Date
- 2013-10-30
- Peptides
- Naphthalene 1,2-dioxygenase subunit alpha: ACE
Naphthalene 1,2-dioxygenase subunit beta: BDF - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
AE
AB
BD
BF
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.50 Å
- Oligo State
- hetero-3-3-mer
- Ligands
- 24 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 12 x SO4: SULFATE ION(Non-functional Binders)
- 3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 3 x FE: FE (III) ION(Non-covalent)
- 3 x 16N: 2,3-dihydro-1H-indene(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ferraro, D.J. et al., One enzyme, many reactions: structural basis for the various reactions catalyzed by naphthalene 1,2-dioxygenase. Iucrj (2017)
- Release Date
- 2013-10-30
- Peptides
- Naphthalene 1,2-dioxygenase subunit alpha: ACE
Naphthalene 1,2-dioxygenase subunit beta: BDF - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
AE
AB
BD
BF
B