SMTL ID : 8yb0.2 (1 other biounit)

XFEL crystal structure of the reduced form of F393H P450BM3 with N-enanthyl-L-prolyl-L-phenylalanine in complex with styrene

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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, F.107, I.153, F.261, A.264, G.265, T.268, T.269, L.272, T.327, A.328, F.331, P.392, H.393, G.394, R.398, A.399, C.400, I.401, G.402, A.406 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:L.86, A:F.87, A:F.87, A:F.87, A:F.107, A:I.153, A:F.261, A:F.261, A:L.272, A:A.328, A:I.401 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 pi-Cation interactions: A:H.393 Metal complexes: A:C.400

1 x D0L: (2S)-2-[[(2S)-1-heptylpyrrolidin-2-yl]carbonylamino]-3-phenyl-propanoic acid(Non-covalent)

D0L.2: 18 residues within 4Å: Chain A: L.20, P.25, V.26, L.29, F.42, A.44, R.47, T.49, Y.51, S.72, Q.73, A.74, F.87, L.188, A.330, M.354, L.437 Ligands: SYN.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.20, A:P.25, A:V.26, A:F.42, A:A.44, A:T.49, A:A.74, A:F.87, A:L.188 Hydrogen bonds: A:Y.51, A:Q.73, A:A.74 Salt bridges: A:R.47 pi-Cation interactions: A:R.47

1 x SYN: ethenylbenzene(Non-covalent)

SYN.3: 7 residues within 4Å: Chain A: V.78, A.82, F.87, I.263, A.264, T.438 Ligands: D0L.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.78, A:A.82, A:F.87, A:F.87, A:F.87, A:I.263, A:A.264, A:T.438

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: V.308, K.309, L.311, K.312, G.315, T.411 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.309 Water bridges: A:G.315 GOL.5: 5 residues within 4Å: Chain A: R.79, G.83, D.84, E.252, Y.256 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.79 Water bridges: A:D.84 GOL.6: 4 residues within 4Å: Chain A: N.319, F.379, P.382, F.390 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.319 Water bridges: A:N.319, A:F.379 GOL.7: 6 residues within 4Å: Chain A: M.5, K.41, R.50, P.346, L.347, D.351 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.41, A:R.50, A:R.50 GOL.8: 5 residues within 4Å: Chain A: D.68, T.91, H.92, Y.334, K.336 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.336, A:K.336 Water bridges: A:Q.397

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagao, S. et al., XFEL Crystallography Reveals Dynamic Control of Non-Natural Substrate Binding in Cytochrome P450BM3 Catalytic Cycle. To Be Published

Release Date

2025-02-12

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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