SMTL ID : 1eg9.2 (1 other biounit)

NAPHTHALENE 1,2-DIOXYGENASE WITH INDOLE BOUND IN THE ACTIVE SITE.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-6-6-mer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: L.128, N.129, K.130, K.131 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain B: Q.63, Q.65 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain B: G.59, S.60, E.61, K.164, K.172 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain C: L.128, N.129, K.130, K.131 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain D: Q.63, Q.65 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain D: G.59, S.60, E.61, K.164, K.172 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain E: L.128, N.129, K.130, K.131 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain F: Q.63, Q.65 Ligand excluded by PLIP SO4.18: 5 residues within 4Å: Chain F: G.59, S.60, E.61, K.164, K.172 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain G: L.128, N.129, K.130, K.131 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain H: Q.63, Q.65 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain H: G.59, S.60, E.61, K.164, K.172 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain I: L.128, N.129, K.130, K.131 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain J: Q.63, Q.65 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain J: G.59, S.60, E.61, K.164, K.172 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain K: L.128, N.129, K.130, K.131 Ligand excluded by PLIP SO4.35: 2 residues within 4Å: Chain L: Q.63, Q.65 Ligand excluded by PLIP SO4.36: 5 residues within 4Å: Chain L: G.59, S.60, E.61, K.164, K.172 Ligand excluded by PLIP

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

FE.2: 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.17 FE.8: 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.14: 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.64 FE.20: 4 residues within 4Å: Chain G: N.201, H.208, H.213, D.362 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.208, G:H.213, G:D.362, G:D.362, H2O.88 FE.26: 4 residues within 4Å: Chain I: N.201, H.208, H.213, D.362 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:H.208, I:H.213, I:D.362, I:D.362, H2O.111 FE.32: 4 residues within 4Å: Chain K: N.201, H.208, H.213, D.362 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:H.208, K:H.213, K:D.362, K:D.362, H2O.135

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

FES.3: 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.9: 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.15: 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 FES.21: 10 residues within 4Å: Chain G: 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 G, Metal complexes: G:C.81, G:H.83, G:C.101, G:H.104 FES.27: 10 residues within 4Å: Chain I: 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 I, Metal complexes: I:C.81, I:H.83, I:C.101, I:H.104 FES.33: 10 residues within 4Å: Chain K: 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 K, Metal complexes: K:C.81, K:H.83, K:C.101, K:H.104

6 x IND: INDOLE(Non-covalent)

IND.4: 7 residues within 4Å: Chain A: N.201, D.205, H.208, V.209, H.295, N.297, L.307 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.209, A:N.297, A:L.307 Hydrogen bonds: A:N.201, A:N.297 pi-Stacking: A:H.208 IND.10: 7 residues within 4Å: Chain C: N.201, D.205, H.208, V.209, H.295, N.297, L.307 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.209, C:N.297, C:L.307 Hydrogen bonds: C:N.201, C:N.297 pi-Stacking: C:H.208 IND.16: 7 residues within 4Å: Chain E: N.201, D.205, H.208, V.209, H.295, N.297, L.307 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:V.209, E:N.297, E:L.307 Hydrogen bonds: E:N.201, E:N.297 pi-Stacking: E:H.208 IND.22: 7 residues within 4Å: Chain G: N.201, D.205, H.208, V.209, H.295, N.297, L.307 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:V.209, G:N.297, G:L.307 Hydrogen bonds: G:N.201, G:N.297 pi-Stacking: G:H.208 IND.28: 7 residues within 4Å: Chain I: N.201, D.205, H.208, V.209, H.295, N.297, L.307 6 PLIP interactions: 6 interactions with chain I Hydrophobic interactions: I:V.209, I:N.297, I:L.307 Hydrogen bonds: I:N.201, I:N.297 pi-Stacking: I:H.208 IND.34: 7 residues within 4Å: Chain K: N.201, D.205, H.208, V.209, H.295, N.297, L.307 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:V.209, K:N.297, K:L.307 Hydrogen bonds: K:N.201, K:N.297 pi-Stacking: K:H.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carredano, E. et al., Substrate binding site of naphthalene 1,2-dioxygenase: functional implications of indole binding. J.Mol.Biol. (2000)

Release Date

2000-05-24

Peptides

PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT): ACEGIK
PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT): BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

I
A

K
A

B
B

D
B

F
B

H
B

J
B

L
B

PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT)

PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT)

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