SMTL ID : 8yb3.2 (1 other biounit)

XFEL crystal structure of the oxygen-bound form of F87A/F393H P450BM3 with N-enanthyl-L-prolyl-L-phenylalanine in complex with styrene

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

HEM.1: 26 residues within 4Å: Chain A: K.69, L.75, L.86, A.87, W.96, F.107, 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 Ligands: SYN.3, OXY.4 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:L.86, A:A.87, A:F.107, A:F.261, A:F.261, A:A.264, A:L.272, A:A.328, A:I.401 Water bridges: A:K.69, A:K.69, A:S.72, 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: 17 residues within 4Å: Chain A: L.20, P.25, V.26, L.29, F.42, R.47, T.49, Y.51, S.72, Q.73, A.74, L.188, A.328, A.330, M.354, L.437 Ligands: SYN.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.20, A:P.25, A:V.26, A:F.42, A:T.49, A:A.74, A:L.188, A:A.328 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: A.87, I.263, A.264, T.438 Ligands: HEM.1, D0L.2, OXY.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.87, A:I.263, A:A.264, A:T.438

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.4: 4 residues within 4Å: Chain A: A.264, T.268 Ligands: HEM.1, SYN.3 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: W.130, E.131, L.133, N.134, F.421, A.448, K.449, S.450 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.448, A:S.450 Water bridges: A:E.131, A:E.131, A:A.448 GOL.6: 6 residues within 4Å: Chain A: D.68, T.91, H.92, Y.334, K.336, Q.397 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.334, A:Y.334, A:K.336 GOL.7: 7 residues within 4Å: Chain A: K.391, H.393, G.394, N.395, G.396, A.399, Q.403 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.391, A:G.396, A:Q.403 Water bridges: A:F.390, A:K.391, A:H.393, A:N.395 GOL.8: 7 residues within 4Å: Chain A: V.308, K.309, L.311, K.312, G.315, L.407, T.411 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.309, A:K.309, A:L.311

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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