SMTL ID : 6llf.1

Biphenyl-2,2',3-triol-soaked resting complex of Oxy and Fd in carbazole 1,9a-dioxygenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

hetero-3-3-mer

Ligands

6 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.13: 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.22: 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.30: 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.32: 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 FES.34: 9 residues within 4Å: Chain F: 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 F, Metal complexes: F:C.46, F:H.48, F:C.65, F:H.68

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

FE2.2: 4 residues within 4Å: Chain A: H.183, H.187, D.333 Ligands: WBP.3 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.1 FE2.14: 4 residues within 4Å: Chain B: H.183, H.187, D.333 Ligands: WBP.15 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.17 FE2.23: 4 residues within 4Å: Chain C: H.183, H.187, D.333 Ligands: WBP.24 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.29

3 x WBP: 3-(2-hydroxyphenyl)benzene-1,2-diol(Non-covalent)

WBP.3: 13 residues within 4Å: Chain A: H.183, I.184, L.200, A.259, I.262, V.272, F.275, Q.282, E.284, F.329, N.330, D.333 Ligands: FE2.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.184, A:L.200, A:A.259, A:I.262, A:V.272, A:V.272, A:F.275, A:F.275, A:F.329 Hydrogen bonds: A:N.330 Water bridges: A:G.178 pi-Stacking: A:F.329 WBP.15: 15 residues within 4Å: Chain B: G.178, H.183, I.184, L.200, A.259, I.262, L.270, V.272, F.275, Q.282, E.284, Y.286, F.329, N.330 Ligands: FE2.14 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.184, B:L.200, B:A.259, B:I.262, B:V.272, B:V.272, B:F.275, B:F.329, B:F.329 Hydrogen bonds: B:E.284 Water bridges: B:G.178, B:D.180, B:D.180, B:H.183, B:N.330 pi-Stacking: B:F.275 WBP.24: 15 residues within 4Å: Chain C: G.178, H.183, I.184, L.200, A.259, I.262, L.270, V.272, F.275, Q.282, E.284, Y.286, F.329, N.330 Ligands: FE2.23 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:I.184, C:L.200, C:A.259, C:I.262, C:V.272, C:F.275, C:F.329, C:F.329 Hydrogen bonds: C:E.284, C:Y.286, C:N.330 Water bridges: C:G.178, C:H.183, C:H.183 pi-Stacking: C:F.275

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

EDO.4: 5 residues within 4Å: Chain A: K.130, M.158, E.159, I.160, L.161 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: L.9, P.17, D.20 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: R.68, G.73, S.383 Chain C: F.343, D.346 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: Y.228 Ligands: EDO.10 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: R.215, Y.228 Ligands: EDO.9 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: C.82, K.83, T.84, K.85 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: D.342, F.343 Chain B: R.68, G.73, S.383 Ligand excluded by PLIP EDO.19: 9 residues within 4Å: Chain B: K.163, Q.165, Y.296, Q.298, L.326, E.327, N.330, N.331, I.334 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain B: K.188, D.189, S.190, I.191, V.193, K.194, R.249 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: D.101, G.102, K.120, L.121, K.122, T.123 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain C: F.204, D.229, L.230, I.231, G.232, A.259 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain B: Y.185, I.186, K.188, W.335 Chain C: K.79, E.81, W.91 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: T.242 Chain C: D.106, I.107, L.108, P.111, I.116 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain C: L.9, A.16, P.17, D.20 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain D: G.17, T.18, I.19, G.56, T.57, L.58 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain E: K.106, L.108 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain F: G.17, I.19, G.56, T.57, L.58 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: V.32, M.33, E.37, K.44, N.164, Y.295 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.44, A:K.44, A:N.164 Water bridges: A:I.166, A:Y.295, A:Y.295 GOL.12: 5 residues within 4Å: Chain A: S.86, T.87, R.98, C.105 Chain C: G.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.86, A:S.86, A:R.98 GOL.18: 3 residues within 4Å: Chain B: W.335 Chain C: V.78, K.79 No protein-ligand interaction detected (PLIP) GOL.29: 4 residues within 4Å: Chain C: Q.119, K.120 Chain E: T.85, V.86 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.120, C:K.120 Water bridges: C:Q.119

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 8 residues within 4Å: Chain A: F.204, D.229, L.230, I.231, G.232, E.233, N.260, I.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.233 Water bridges: A:P.181

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

PEG.16: 3 residues within 4Å: Chain A: W.335 Chain B: V.78, K.79 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y.X. et al., Biphenyl-2,2',3-triol-soaked resting complex of Oxy and Fd in carbazole 1,9a-dioxygenase. To Be Published

Release Date

2021-01-27

Peptides

Terminal oxygenase component of carbazole: ABC
Ferredoxin CarAc: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Terminal oxygenase component of carbazole

Ferredoxin CarAc

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