SMTL ID : 7bui.1

Complex of reduced oxygenase and oxidized ferredoxin in carbazole 1,9a- dioxygenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-3-2-mer

Ligands

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

FES.1: 9 residues within 4Å: Chain A: C.69, H.71, R.72, V.74, C.90, Y.92, H.93, A.94, W.95 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.69, A:H.71, A:C.90, A:H.93 FES.6: 9 residues within 4Å: Chain B: C.69, H.71, R.72, V.74, C.90, Y.92, H.93, A.94, W.95 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.69, B:H.71, B:C.90, B:H.93 FES.13: 9 residues within 4Å: Chain C: C.69, H.71, R.72, V.74, C.90, Y.92, H.93, A.94, W.95 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.69, C:H.71, C:C.90, C:H.93 FES.18: 9 residues within 4Å: Chain D: C.46, H.48, G.49, A.51, C.65, F.67, H.68, G.70, C.84 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.46, D:H.48, D:C.65, D:H.68 FES.19: 9 residues within 4Å: Chain E: C.46, H.48, G.49, A.51, C.65, F.67, H.68, G.70, C.84 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.46, E:H.48, E:C.65, E:H.68

3 x FE2: FE (II) ION(Non-covalent)

FE2.2: 3 residues within 4Å: Chain A: H.183, H.187, D.333 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.183, A:H.187, A:D.333, A:D.333, H2O.4 FE2.7: 3 residues within 4Å: Chain B: H.183, H.187, D.333 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.183, B:H.187, B:D.333, B:D.333, H2O.11 FE2.14: 3 residues within 4Å: Chain C: H.183, H.187, D.333 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.183, C:H.187, C:D.333, C:D.333, H2O.17

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

EDO.3: 6 residues within 4Å: Chain A: G.244 Chain B: S.86, T.87, R.98, C.105, D.106 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.244, B:S.86, B:S.86 EDO.4: 4 residues within 4Å: Chain A: V.32, M.33, E.37, N.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.32, A:N.164, A:N.164 EDO.5: 4 residues within 4Å: Chain A: L.9, A.16, P.17, D.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.20, A:D.20 EDO.9: 4 residues within 4Å: Chain B: K.47, G.50, Q.379, V.382 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.47, B:K.47, B:Q.379 EDO.10: 4 residues within 4Å: Chain B: K.168, S.169, N.292, V.341 No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain B: L.9, A.16, P.17, D.20 No protein-ligand interaction detected (PLIP) EDO.12: 3 residues within 4Å: Chain B: F.34, L.161, G.162 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.162, B:G.162 Water bridges: B:G.131 EDO.15: 4 residues within 4Å: Chain B: D.342 Chain C: K.47, N.52, Q.75 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.47, C:N.52, C:N.52 Water bridges: C:Q.75 EDO.16: 2 residues within 4Å: Chain C: K.79, V.80 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.80 Water bridges: C:K.79 EDO.17: 5 residues within 4Å: Chain C: D.189, S.190, I.191, G.328, D.332 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.191, C:D.332

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 5 residues within 4Å: Chain B: V.32, M.33, E.37, N.164, I.166 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.164 Water bridges: B:I.166 PEG.20: 4 residues within 4Å: Chain E: W.5, E.94, K.96, Y.101 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsuzawa, J. et al., Complex of reduced oxygenase and oxidized ferredoxin in carbazole 1,9a- dioxygenase. To Be Published

Release Date

2021-04-07

Peptides

Terminal oxygenase component of carbazole: ABC
Ferredoxin CarAc: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Terminal oxygenase component of carbazole

Ferredoxin CarAc

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