SMTL ID : 6llh.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

hetero-3-3-mer

Ligands

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

FE2.1: 4 residues within 4Å: Chain A: H.183, H.187, D.333 Ligands: BPY.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.183, A:H.187, A:D.333, A:D.333 FE2.9: 4 residues within 4Å: Chain B: H.183, H.187, D.333 Ligands: BPY.11 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 FE2.18: 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.28

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

FES.2: 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.10: 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.19: 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.25: 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.26: 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.29: 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 BPY: BIPHENYL-2,3-DIOL(Non-covalent)

BPY.3: 13 residues within 4Å: Chain A: H.183, I.184, H.187, A.259, I.262, L.270, V.272, F.275, E.284, F.329, N.330, D.333 Ligands: FE2.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.184, A:A.259, A:I.262, A:L.270, A:V.272, A:F.275, A:F.329 Hydrogen bonds: A:N.330 BPY.11: 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: FE2.9 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.184, B:L.200, B:A.259, B:I.262, B:V.272, B:F.275, B:F.329, B:F.329 Hydrogen bonds: B:G.178 Water bridges: B:N.177, B:G.178, B:H.183, B:H.183, B:N.330 pi-Stacking: B:F.275 BPY.20: 14 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 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:I.184, C:L.200, C:A.259, C:I.262, C:V.272, C:V.272, C:F.275, C:F.329, C:F.329 Hydrogen bonds: C:G.178 Water bridges: C:G.178, C:D.180, C:H.183, C:N.330, C:N.330 pi-Stacking: C:F.275

10 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.158, A:I.160 EDO.8: 4 residues within 4Å: Chain A: F.34, K.36, L.161, G.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.36, A:G.162, A:G.162 Water bridges: A:G.131 EDO.12: 9 residues within 4Å: Chain B: K.163, Q.165, Y.296, Q.298, L.326, E.327, N.330, N.331, I.334 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.163, B:K.163, B:Q.298, B:N.330 Water bridges: B:Q.165 EDO.14: 4 residues within 4Å: Chain A: D.342, F.343 Chain B: R.68, S.383 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.68 Water bridges: A:D.346 EDO.15: 5 residues within 4Å: Chain B: K.61, L.62, Y.63, P.125, V.126 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.61, B:L.62, B:V.126 EDO.16: 7 residues within 4Å: Chain B: F.204, D.229, L.230, I.231, G.232, A.259, N.260 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.229, B:G.232 Water bridges: B:E.233 EDO.17: 4 residues within 4Å: Chain B: F.34, K.36, L.161, G.162 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.162, B:G.162 EDO.21: 6 residues within 4Å: Chain C: F.204, D.229, L.230, I.231, G.232, A.259 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.229, C:G.232, C:A.259 EDO.23: 6 residues within 4Å: Chain B: T.242 Chain C: D.106, I.107, L.108, P.111, I.116 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:I.107, B:T.242, B:T.242 EDO.24: 7 residues within 4Å: Chain B: Y.185, I.186, K.188, W.335 Chain C: K.79, E.81, W.91 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:K.79, C:K.79, C:W.91, B:K.188 Water bridges: B:D.189

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

PGE.5: 10 residues within 4Å: Chain A: F.204, D.229, L.230, I.231, G.232, E.233, A.259, N.260, D.261, I.262 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.260, A:I.262 PGE.28: 6 residues within 4Å: Chain C: R.118 Chain E: E.43, L.88, G.89, K.106, K.107 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:K.107 Water bridges: C:R.118

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 3 residues within 4Å: Chain A: S.86, R.98, C.105 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:R.98 Hydrogen bonds: A:R.98 Water bridges: C:G.244

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

PEG.7: 3 residues within 4Å: Chain A: T.242 Chain B: P.111, T.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.242, A:T.242 PEG.13: 6 residues within 4Å: Chain A: G.244 Chain B: S.86, T.87, R.98, C.105, D.106 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.244, B:S.86, B:S.86, B:R.98, B:D.106 PEG.27: 4 residues within 4Å: Chain E: W.5, E.94, K.96, Y.101 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.94, E:K.96

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.22: 6 residues within 4Å: Chain C: V.32, M.33, E.37, N.164, Q.165, Y.295 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.37, C:N.164, C:N.164 Water bridges: C:V.32, C:I.166, C:Y.295

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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