SMTL ID : 4hm0.1

Naphthalene 1,2-Dioxygenase bound to indole-3-acetate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-3-3-mer

Ligands

45 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 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 PLIP EDO.2: 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 PLIP EDO.3: 2 residues within 4Å: Chain A: E.24, K.374 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: V.183, R.342, D.346 Chain B: N.82 Ligand excluded by PLIP EDO.10: 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 PLIP EDO.11: 7 residues within 4Å: Chain A: D.361, D.364, N.365 Chain B: W.108, G.109, R.148 Chain E: S.102 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: E.142, S.143 Ligands: EDO.13 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: S.73, I.74, V.141, E.142, S.143 Ligands: EDO.12 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: D.396, A.397, V.398, P.400 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: D.46, R.115, F.116 Ligands: EDO.66 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: Y.50, Y.88, Q.102, M.191, V.192, F.193 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain B: N.91, Q.94 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain B: R.138, A.158, E.160, F.177, V.178, D.179 Ligands: EDO.39 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: V.190 Chain B: Q.186, T.187, H.188 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: T.35, T.39, I.120, V.123 Chain F: T.121, N.122 Ligand excluded by PLIP EDO.24: 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 PLIP EDO.25: 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 PLIP EDO.26: 2 residues within 4Å: Chain C: E.24, K.374 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain C: V.183, R.342, D.346 Chain D: N.82 Ligand excluded by PLIP EDO.33: 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 PLIP EDO.34: 7 residues within 4Å: Chain A: S.102 Chain C: D.361, D.364, N.365 Chain D: W.108, G.109, R.148 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain C: E.142, S.143 Ligands: EDO.36 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain C: S.73, I.74, V.141, E.142, S.143 Ligands: EDO.35 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain C: D.396, A.397, V.398, P.400 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain D: D.46, R.115, F.116 Ligands: EDO.20 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain D: Y.50, Y.88, Q.102, M.191, V.192, F.193 Ligand excluded by PLIP EDO.42: 2 residues within 4Å: Chain D: N.91, Q.94 Ligand excluded by PLIP EDO.43: 7 residues within 4Å: Chain D: R.138, A.158, E.160, F.177, V.178, D.179 Ligands: EDO.62 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain C: V.190 Chain D: Q.186, T.187, H.188 Ligand excluded by PLIP EDO.45: 6 residues within 4Å: Chain B: T.121, N.122 Chain D: T.35, T.39, I.120, V.123 Ligand excluded by PLIP EDO.47: 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 PLIP EDO.48: 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 PLIP EDO.49: 2 residues within 4Å: Chain E: E.24, K.374 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain E: V.183, R.342, D.346 Chain F: N.82 Ligand excluded by PLIP EDO.56: 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 PLIP EDO.57: 7 residues within 4Å: Chain C: S.102 Chain E: D.361, D.364, N.365 Chain F: W.108, G.109, R.148 Ligand excluded by PLIP EDO.58: 3 residues within 4Å: Chain E: E.142, S.143 Ligands: EDO.59 Ligand excluded by PLIP EDO.59: 6 residues within 4Å: Chain E: S.73, I.74, V.141, E.142, S.143 Ligands: EDO.58 Ligand excluded by PLIP EDO.60: 4 residues within 4Å: Chain E: D.396, A.397, V.398, P.400 Ligand excluded by PLIP EDO.62: 4 residues within 4Å: Chain F: D.46, R.115, F.116 Ligands: EDO.43 Ligand excluded by PLIP EDO.64: 6 residues within 4Å: Chain F: Y.50, Y.88, Q.102, M.191, V.192, F.193 Ligand excluded by PLIP EDO.65: 2 residues within 4Å: Chain F: N.91, Q.94 Ligand excluded by PLIP EDO.66: 7 residues within 4Å: Chain F: R.138, A.158, E.160, F.177, V.178, D.179 Ligands: EDO.16 Ligand excluded by PLIP EDO.67: 4 residues within 4Å: Chain E: V.190 Chain F: Q.186, T.187, H.188 Ligand excluded by PLIP EDO.68: 6 residues within 4Å: Chain D: T.121, N.122 Chain F: T.35, T.39, I.120, V.123 Ligand excluded by PLIP

3 x FE: FE (III) ION(Non-covalent)

FE.4: 5 residues within 4Å: Chain A: N.201, H.208, H.213, D.362 Ligands: IAC.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.208, A:H.213, A:D.362, A:D.362 FE.27: 5 residues within 4Å: Chain C: N.201, H.208, H.213, D.362 Ligands: IAC.28 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.208, C:H.213, C:D.362, C:D.362 FE.50: 5 residues within 4Å: Chain E: N.201, H.208, H.213, D.362 Ligands: IAC.51 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.208, E:H.213, E:D.362, E:D.362

3 x IAC: 1H-INDOL-3-YLACETIC ACID(Non-covalent)

IAC.5: 14 residues within 4Å: Chain A: N.201, F.202, D.205, H.208, V.209, H.213, F.224, L.253, H.295, N.297, L.307, F.352, D.362 Ligands: FE.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.202, A:V.209, A:F.224, A:L.253, A:L.307 Hydrogen bonds: A:N.201, A:N.297 Salt bridges: A:H.208, A:H.213 pi-Stacking: A:H.208 IAC.28: 14 residues within 4Å: Chain C: N.201, F.202, D.205, H.208, V.209, H.213, F.224, L.253, H.295, N.297, L.307, F.352, D.362 Ligands: FE.27 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.202, C:V.209, C:F.224, C:L.253, C:L.307 Hydrogen bonds: C:N.201, C:N.297 Salt bridges: C:H.208, C:H.213 pi-Stacking: C:H.208 IAC.51: 14 residues within 4Å: Chain E: N.201, F.202, D.205, H.208, V.209, H.213, F.224, L.253, H.295, N.297, L.307, F.352, D.362 Ligands: FE.50 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:F.202, E:V.209, E:F.224, E:L.253, E:L.307 Hydrogen bonds: E:N.201, E:N.297 Salt bridges: E:H.208, E:H.213 pi-Stacking: E:H.208

15 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 2 residues within 4Å: Chain A: K.245, W.439 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.394, A:Y.394 Salt bridges: A:K.245 SO4.7: 4 residues within 4Å: Chain A: L.128, N.129, K.130, K.131 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.130, A:K.131 Water bridges: A:K.130, A:K.130 Salt bridges: A:K.130, A:K.131 SO4.15: 2 residues within 4Å: Chain A: P.337, E.338 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.338 Water bridges: A:M.336, A:E.338, A:D.339 SO4.17: 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 SO4.23: 4 residues within 4Å: Chain B: K.132, E.133, R.165, R.171 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.165, B:R.171 SO4.29: 2 residues within 4Å: Chain C: K.245, W.439 3 PLIP interactions: 3 interactions with chain C Water bridges: C:Y.394, C:Y.394 Salt bridges: C:K.245 SO4.30: 4 residues within 4Å: Chain C: L.128, N.129, K.130, K.131 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.130, C:K.131 Water bridges: C:K.130, C:K.130 Salt bridges: C:K.130, C:K.131 SO4.38: 2 residues within 4Å: Chain C: P.337, E.338 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.338 Water bridges: C:M.336, C:E.338, C:D.339 SO4.40: 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 SO4.46: 4 residues within 4Å: Chain D: K.132, E.133, R.165, R.171 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.165, D:R.171 SO4.52: 2 residues within 4Å: Chain E: K.245, W.439 3 PLIP interactions: 3 interactions with chain E Water bridges: E:Y.394, E:Y.394 Salt bridges: E:K.245 SO4.53: 4 residues within 4Å: Chain E: L.128, N.129, K.130, K.131 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:K.130, E:K.131 Water bridges: E:K.130, E:K.130 Salt bridges: E:K.130, E:K.131 SO4.61: 2 residues within 4Å: Chain E: P.337, E.338 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.338 Water bridges: E:M.336, E:E.338, E:D.339 SO4.63: 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 SO4.69: 4 residues within 4Å: Chain F: K.132, E.133, R.165, R.171 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:R.165, F:R.171

3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.8: 9 residues within 4Å: Chain A: C.81, H.83, R.84, G.85, 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.31: 9 residues within 4Å: Chain C: C.81, H.83, R.84, G.85, 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.54: 9 residues within 4Å: Chain E: C.81, H.83, R.84, G.85, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferraro, D.J. et al., Naphthalene 1,2-Dioxygenase bound to indole-3-acetate. To be Published

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
A

C
A

E
A

B
B

D
B

F
B

Naphthalene 1,2-dioxygenase subunit alpha

Naphthalene 1,2-dioxygenase subunit beta

Related Entries With Identical Sequence