SMTL ID : 7w9d.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

MI9.1: 25 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, 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 23 PLIP interactions: 23 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:A.329, A:F.394, A:I.402, A:F.406, A:A.407 Water bridges: A:K.70, A:K.70, A:H.101, A:S.333, A:S.333, A:S.333, A:R.399 Salt bridges: A:K.70, A:R.399 MI9.5: 26 residues within 4Å: Chain B: 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 B Hydrophobic interactions: B:L.87, B:F.88, B:F.88, B:F.88, B:F.108, B:F.262, B:F.262, B:A.265, B:L.273, B:L.323, B:A.329, B:F.394, B:I.402, B:F.406, B:A.407 Hydrogen bonds: B:R.399 Water bridges: B:K.70, B:K.70, B:H.101, B:S.333, B:S.333, B:S.333 Salt bridges: B:K.70, B:R.399

2 x 8PD: (2~{S})-2-(hexadecanoylamino)-4-oxidanyl-butanoic acid(Non-covalent)

8PD.2: 17 residues within 4Å: Chain A: L.21, V.27, L.30, R.48, Y.52, S.73, Q.74, A.75, V.79, A.83, F.88, L.189, T.261, I.264, A.329, A.331, L.438 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.21, A:V.27, A:A.83, A:F.88, A:F.88, A:I.264, A:A.329, A:A.331 Hydrogen bonds: A:R.48, A:R.48, A:Y.52, A:Q.74, A:A.75 8PD.6: 18 residues within 4Å: Chain B: L.21, V.27, L.30, R.48, Y.52, S.73, Q.74, A.75, V.79, A.83, F.88, L.189, T.261, I.264, A.265, P.330, A.331, L.438 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.21, B:V.27, B:A.83, B:F.88, B:F.88, B:I.264, B:A.265, B:A.331 Hydrogen bonds: B:R.48, B:R.48, B:Y.52, B:Q.74, B:A.75

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.48, V.49, R.51, G.351, D.352, E.353 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.49, A:R.51, A:D.352, A:D.352, A:E.353 Water bridges: A:G.351, A:D.352 GOL.4: 6 residues within 4Å: Chain A: K.392, G.395, N.396, G.397, A.400, Q.404 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.392, A:N.396, A:G.397, A:Q.404, A:Q.404 GOL.7: 3 residues within 4Å: Chain B: H.286, Q.289, K.290 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.290, B:K.290 GOL.8: 6 residues within 4Å: Chain B: K.392, F.394, G.395, N.396, G.397, Q.404 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.392, B:K.392, B:G.397, B:Q.404 Water bridges: B:N.396, B:N.396, B:G.397, B:Q.404

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-Hexadecanoyl-L-Homoserine. 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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