SMTL ID : 7w97.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 25 residues within 4Å: Chain A: K.70, L.76, L.87, F.88, W.97, F.108, I.154, 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, A.407 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:L.87, A:F.88, A:F.88, A:F.108, A:I.154, A:F.262, A:F.262, A:A.265, A:L.273, A:A.329, A:F.394, A:I.402 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 Metal complexes: A:C.401 HEM.3: 25 residues within 4Å: Chain B: K.70, L.76, L.87, F.88, W.97, F.108, I.154, 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, A.407 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:L.87, B:F.88, B:F.88, B:F.88, B:F.108, B:I.154, B:F.262, B:F.262, B:A.265, B:L.273, B:A.329, B:F.394, B:I.402 Hydrogen bonds: B:R.399 Water bridges: B:K.70, B:K.70, B:S.333, B:S.333, B:S.333, B:S.333 Salt bridges: B:K.70, B:R.399 Metal complexes: B:C.401

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, Y.52, S.73, Q.74, A.75, V.79, A.83, F.88, L.189, I.264, A.265, A.329, A.331, L.438, T.439 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.21, A:V.27, A:V.79, A:A.83, A:F.88, A:F.88, A:I.264, A:A.265, A:A.329, A:L.438, A:T.439 Hydrogen bonds: A:Y.52, A:Q.74, A:A.75 Water bridges: A:R.48 8PD.4: 15 residues within 4Å: Chain B: L.21, V.27, L.30, Y.52, S.73, Q.74, A.75, V.79, A.83, F.88, L.189, I.264, A.329, A.331, L.438 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.21, B:V.27, B:V.79, B:A.83, B:F.88, B:F.88, B:I.264, B:A.329 Hydrogen bonds: B:Q.74, B:A.75 Water bridges: B:R.48, B:R.48

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: E.381 Chain B: K.392, G.395, N.396, G.397, A.400, Q.404 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.396, B:G.397, B:Q.404, B:Q.404 Water bridges: B:H.389, B:F.391, B:N.396 GOL.6: 5 residues within 4Å: Chain B: V.309, K.310, L.312, G.316, T.412 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.310, B:K.310, B:K.310

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karasawa, M. et al., Crystal Structure of the 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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