SMTL ID : 7w9j.1

Crystal Structure of the Oxomolybdenum Mesoporphyrin IX-Reconstituted CYP102A1 (P450BM3) Heme Domain with N-Dodecanoyl-L-Homoserine Lactone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x MI9: Oxomolybdenum Mesoporphyrin IX(Non-covalent)

MI9.1: 26 residues within 4Å: Chain A: K.70, L.76, L.87, F.88, W.97, F.108, F.262, A.265, G.266, T.269, T.270, L.273, L.323, T.328, A.329, F.332, P.393, F.394, G.395, R.399, A.400, C.401, I.402, G.403, F.406, A.407 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:L.87, A:F.88, A:F.88, A:F.88, A:F.108, A:F.262, A:F.262, A:A.265, A:L.273, A:L.323, A:A.329, A:F.394, A:I.402, A:F.406, A:A.407 Hydrogen bonds: A:T.269 Water bridges: A:K.70, A:K.70, A:H.101, A:S.333, A:S.333, A:S.333 Salt bridges: A:K.70, A:R.399 MI9.5: 25 residues within 4Å: Chain B: K.70, L.76, L.87, F.88, W.97, F.108, F.262, A.265, T.269, T.270, L.273, T.328, A.329, F.332, P.393, F.394, G.395, R.399, A.400, C.401, I.402, G.403, F.406, A.407 Ligands: EWM.6 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:L.87, B:F.88, B:F.88, B:F.88, B:F.108, B:F.262, B:A.265, B:L.273, B:F.394, B:I.402, B:F.406, B:A.407 Water bridges: B:K.70, B:K.70, B:S.333, B:S.333, B:S.333, B:R.399 Salt bridges: B:K.70, B:R.399

2 x EWM: N-[(3S)-2-oxooxolan-3-yl]dodecanamide(Non-covalent)

EWM.2: 13 residues within 4Å: Chain A: P.26, L.30, Y.52, S.73, A.75, V.79, A.83, F.88, L.189, T.261, I.264, A.331, L.438 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.83, A:F.88, A:F.88, A:I.264, A:A.331 Hydrogen bonds: A:S.73 Water bridges: A:A.75, A:L.438 EWM.6: 14 residues within 4Å: Chain B: P.26, L.30, Y.52, S.73, A.75, F.88, M.186, I.264, A.265, A.329, A.331, L.438, T.439 Ligands: MI9.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.88, B:F.88, B:F.88, B:I.264, B:A.329, B:L.438, B:T.439 Hydrogen bonds: B:S.73 Water bridges: B:A.75

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: E.294, R.297, Q.311, K.313 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.297, A:R.297, A:Q.311 GOL.4: 3 residues within 4Å: Chain A: H.286, Q.289, K.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.286, A:K.290 GOL.7: 6 residues within 4Å: Chain B: W.131, L.134, N.135, A.449, K.450, S.451 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.135, B:S.451 Water bridges: B:A.449, B:A.449, B:S.451

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karasawa, M. et al., Crystal Structure of the Oxomolybdenum Mesoporphyrin IX-Reconstituted CYP102A1 (P450BM3) Heme Domain with N-Dodecanoyl-L-Homoserine Lactone. To Be Published

Release Date

2022-12-14

Peptides

Bifunctional cytochrome P450/NADPH--P450 reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional cytochrome P450/NADPH--P450 reductase

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