SMTL ID : 7bug.1

Reduced oxygenase of carbazole 1,9a-dioxygenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

3 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.26: 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

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: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.183, A:H.187, A:D.333, H2O.7, H2O.8 FE2.14: 3 residues within 4Å: Chain B: H.183, H.187, D.333 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.183, B:H.187, B:D.333, H2O.18, H2O.20 FE2.27: 3 residues within 4Å: Chain C: H.183, H.187, D.333 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.183, C:H.187, C:D.333, H2O.30, H2O.31

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 1 residues within 4Å: Chain A: E.100 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.100, H2O.4, H2O.5, H2O.6, H2O.9, H2O.9 MG.15: 1 residues within 4Å: Chain B: E.100 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.100, H2O.14, H2O.17, H2O.21, H2O.22, H2O.23 MG.16: 2 residues within 4Å: Chain B: Y.253, G.254 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:Y.253, H2O.12, H2O.16, H2O.21 MG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain C: E.100 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.100, H2O.28, H2O.29, H2O.31, H2O.32

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

PEG.4: 7 residues within 4Å: Chain A: I.184, A.259, F.275, Q.282, E.284, F.329, N.330 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.284, A:N.330 PEG.19: 6 residues within 4Å: Chain B: A.199, P.201, F.204, V.258, A.259 Ligands: PG0.24 No protein-ligand interaction detected (PLIP) PEG.21: 6 residues within 4Å: Chain B: F.34, K.36, L.161, G.162, F.317, E.318 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.162, B:E.318, B:E.318 PEG.22: 4 residues within 4Å: Chain B: V.216, A.364, K.367, E.371 No protein-ligand interaction detected (PLIP) PEG.29: 4 residues within 4Å: Chain A: D.342 Chain C: K.47, N.52, Q.75 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.47, C:N.52 Water bridges: C:K.47, C:G.50, C:G.50 PEG.31: 5 residues within 4Å: Chain C: F.34, K.36, E.37, L.161, G.162 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.36, C:G.162 PEG.33: 3 residues within 4Å: Chain C: P.111, T.112, S.113 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.106, C:P.111 PEG.34: 6 residues within 4Å: Chain C: A.199, L.200, P.201, V.258, A.259 Ligands: PG0.36 1 PLIP interactions: 1 interactions with chain C Water bridges: C:V.258

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

PGE.5: 4 residues within 4Å: Chain A: E.37, P.43, K.44, T.45 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.37, A:P.43, A:T.45 PGE.7: 5 residues within 4Å: Chain A: R.98, C.105, I.116, G.117, R.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.98 Water bridges: A:R.118 PGE.18: 4 residues within 4Å: Chain B: K.47, N.52, Q.75 Chain C: D.342 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.47, B:N.52 PGE.30: 3 residues within 4Å: Chain C: E.37, K.44, T.45 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.45 Water bridges: C:Y.295

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 7 residues within 4Å: Chain A: K.47, N.52, Q.75, I.289, D.290, T.293 Chain B: D.342 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.47, A:N.52, A:T.293 Water bridges: A:K.47

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.8: 5 residues within 4Å: Chain A: I.58, Y.63, K.85, S.86, E.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.85 Water bridges: A:D.59

3 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.9: 6 residues within 4Å: Chain A: D.195, N.196, K.256, E.316, K.320, W.321 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.320 1PE.20: 3 residues within 4Å: Chain B: K.10, R.11, K.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.10, B:R.11, B:K.13 1PE.32: 5 residues within 4Å: Chain C: I.58, Y.63, K.85, S.86, E.100 No protein-ligand interaction detected (PLIP)

2 x CO3: CARBONATE ION(Non-functional Binders)

CO3.10: 3 residues within 4Å: Chain A: K.61, P.125, V.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.61, A:V.126 Water bridges: A:K.61 CO3.23: 6 residues within 4Å: Chain B: P.151, N.152, F.153, L.154, D.155, R.224 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.152, B:L.154, B:D.155, B:D.155 Water bridges: B:R.224

2 x MXE: 2-METHOXYETHANOL(Non-covalent)

MXE.11: 4 residues within 4Å: Chain A: Q.127, P.144, L.145, A.146 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.127, A:L.145, A:A.146 MXE.35: 2 residues within 4Å: Chain C: A.129, K.130 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.130 Water bridges: C:K.130, C:G.131, C:G.131

4 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.12: 3 residues within 4Å: Chain A: E.40, D.59, G.60 No protein-ligand interaction detected (PLIP) PG0.24: 10 residues within 4Å: Chain B: I.184, A.259, L.270, V.272, F.275, Q.282, E.284, F.329, N.330 Ligands: PEG.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.284, B:N.330 PG0.25: 5 residues within 4Å: Chain A: Q.115 Chain B: L.355, F.356, E.357, V.363 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.115 PG0.36: 10 residues within 4Å: Chain C: I.184, A.259, L.270, V.272, F.275, Q.282, E.284, F.329, N.330 Ligands: PEG.34 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.330

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsuzawa, J. et al., Reduced oxygenase of carbazole 1,9a-dioxygenase. To Be Published

Release Date

2021-04-07

Peptides

Terminal oxygenase component of carbazole: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Terminal oxygenase component of carbazole

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