- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.95 Å
- Oligo State
- hetero-oligomer
- Ligands
- 18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 3 x NDH: (1R, 2S)-CIS 1,2 DIHYDROXY-1,2-DIHYDRONAPHTHALENE(Non-covalent)
NDH.3: 12 residues within 4Å:- Chain A: N.201, F.202, D.205, H.208, V.209, H.213, L.253, H.295, N.297, F.352, D.362
- Ligands: FE.6
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:V.209, A:L.253, A:N.297
- Hydrogen bonds: A:N.201, A:D.362
NDH.15: 12 residues within 4Å:- Chain C: N.201, F.202, D.205, H.208, V.209, H.213, L.253, H.295, N.297, F.352, D.362
- Ligands: FE.18
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:V.209, C:L.253, C:N.297
- Hydrogen bonds: C:N.201, C:D.362
NDH.27: 12 residues within 4Å:- Chain E: N.201, F.202, D.205, H.208, V.209, H.213, L.253, H.295, N.297, F.352, D.362
- Ligands: FE.30
5 PLIP interactions:5 interactions with chain E- Hydrophobic interactions: E:V.209, E:L.253, E:N.297
- Hydrogen bonds: E:N.201, E:D.362
- 9 x SO4: SULFATE ION(Non-functional Binders)
SO4.4: 4 residues within 4Å:- Chain A: L.128, N.129, K.130, K.131
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:L.128, A:K.130, A:K.131
- Salt bridges: A:K.130
SO4.11: 2 residues within 4Å:- Chain B: Q.63, Q.65
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Q.63, B:Q.65
SO4.12: 5 residues within 4Å:- Chain B: G.59, S.60, E.61, E.167, K.172
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
SO4.16: 4 residues within 4Å:- Chain C: L.128, N.129, K.130, K.131
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:L.128, C:K.130, C:K.131
- Salt bridges: C:K.130
SO4.23: 2 residues within 4Å:- Chain D: Q.63, Q.65
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:Q.63, D:Q.65
SO4.24: 5 residues within 4Å:- Chain D: G.59, S.60, E.61, E.167, K.172
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
SO4.28: 4 residues within 4Å:- Chain E: L.128, N.129, K.130, K.131
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:L.128, E:K.130, E:K.131
- Salt bridges: E:K.130
SO4.35: 2 residues within 4Å:- Chain F: Q.63, Q.65
2 PLIP interactions:2 interactions with chain F- Hydrogen bonds: F:Q.63, F:Q.65
SO4.36: 5 residues within 4Å:- Chain F: G.59, S.60, E.61, E.167, K.172
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.5: 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.17: 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.29: 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.6: 5 residues within 4Å:- Chain A: N.201, H.208, H.213, D.362
- Ligands: NDH.3
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:H.208, A:H.213, A:D.362, A:D.362
FE.18: 5 residues within 4Å:- Chain C: N.201, H.208, H.213, D.362
- Ligands: NDH.15
4 PLIP interactions:4 interactions with chain C- Metal complexes: C:H.208, C:H.213, C:D.362, C:D.362
FE.30: 5 residues within 4Å:- Chain E: N.201, H.208, H.213, D.362
- Ligands: NDH.27
4 PLIP interactions:4 interactions with chain E- Metal complexes: E:H.208, E:H.213, E:D.362, E:D.362
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Karlsson, A. et al., Crystal Structure of Naphthalene Dioxygenase: Side-on Binding of Dioxygen to Iron. Science (2003)
- Release Date
- 2003-02-20
- 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 1.95 Å
- Oligo State
- hetero-oligomer
- Ligands
- 18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 3 x NDH: (1R, 2S)-CIS 1,2 DIHYDROXY-1,2-DIHYDRONAPHTHALENE(Non-covalent)
- 9 x SO4: SULFATE ION(Non-functional Binders)
- 3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 3 x FE: FE (III) ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Karlsson, A. et al., Crystal Structure of Naphthalene Dioxygenase: Side-on Binding of Dioxygen to Iron. Science (2003)
- Release Date
- 2003-02-20
- 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