SMTL ID : 9ist.2 (1 other biounit)

Crystal Structure of Cytochrome P450BM3 VI-18A12 Mutant Heme Domain with N-Decanoyl-L-Homoserine Lactone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 25 residues within 4Å: Chain A: K.69, L.75, L.86, F.87, W.96, I.153, F.261, A.264, T.268, T.269, L.272, T.327, A.328, F.331, P.392, F.393, G.394, R.398, A.399, C.400, I.401, G.402, F.405, A.406 Ligands: DMS.3 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:L.86, A:F.87, A:I.153, A:F.261, A:A.264, A:T.268, A:L.272, A:T.327, A:A.328, A:F.393, A:F.393, A:I.401, A:F.405, A:A.406 Water bridges: A:K.69, A:K.69, A:S.332, A:S.332, A:S.332, A:R.398 Salt bridges: A:K.69, A:R.398 Metal complexes: A:C.400

1 x HL0: N-[(3S)-2-oxotetrahydrofuran-3-yl]decanamide(Non-covalent)

HL0.2: 16 residues within 4Å: Chain A: L.29, W.47, L.49, Y.51, S.72, Q.73, V.74, F.87, P.188, Q.189, A.328, P.329, A.330, M.354, L.437 Ligands: DMS.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.47, A:V.74, A:F.87, A:A.328, A:L.437, A:L.437 Hydrogen bonds: A:Y.51, A:S.72, A:V.74 Water bridges: A:Q.189

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 5 residues within 4Å: Chain A: F.87, A.264, T.268 Ligands: HEM.1, HL0.2 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.87

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: K.391, F.393, G.394, N.395, G.396, A.399, Q.403 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.391, A:G.396, A:Q.403, A:Q.403 Water bridges: A:G.394 GOL.5: 7 residues within 4Å: Chain A: T.22, D.23, K.24, V.25, M.185, N.186, E.435 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.22, A:V.25, A:N.186, A:E.435, A:E.435 Water bridges: A:Q.189 GOL.6: 5 residues within 4Å: Chain A: C.62, D.63, E.64, H.388, N.395 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.64, A:N.395, A:N.395 GOL.7: 4 residues within 4Å: Chain A: P.170, I.174, V.178, H.266 No protein-ligand interaction detected (PLIP) GOL.8: 7 residues within 4Å: Chain A: F.67, K.69, L.333, N.395, G.396, Q.397, R.398 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.395, A:N.395, A:Q.397, A:R.398

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yokoyama, Y. et al., Bacterial Acyl Homoserine Lactones Triggered Non-Native Substrate Hydroxylation Catalyzed by Directed-Evolution-Derived Cytochrome P450BM3 Mutants. Chemcatchem (2024)

Release Date

2024-12-04

Peptides

Bifunctional cytochrome P450/NADPH--P450 reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Bifunctional cytochrome P450/NADPH--P450 reductase

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