SMTL ID : 8yay.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 24 residues within 4Å: Chain A: K.69, L.75, L.86, F.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 24 PLIP interactions: 23 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:L.86, A:F.87, A:F.87, A:F.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:H.100, A:S.332, 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, H2O.3 HEM.7: 24 residues within 4Å: Chain B: K.69, L.75, L.86, F.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 22 PLIP interactions: 21 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:L.86, B:F.87, B:F.87, B:F.87, B:F.107, B:F.261, B:F.261, B:A.264, B:L.272, B:A.328, B:I.401 Water bridges: B:K.69, B:K.69, B:S.332, B:S.332, B:S.332, B:R.398 Salt bridges: B:K.69, B:R.398 pi-Cation interactions: B:H.393 Metal complexes: B:C.400, H2O.18

2 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:R.47, A:T.49, A:A.74, A:F.87, A:L.188 Hydrogen bonds: A:Q.73, A:A.74 Salt bridges: A:R.47 pi-Cation interactions: A:R.47 D0L.8: 16 residues within 4Å: Chain B: L.20, P.25, V.26, L.29, F.42, R.47, T.49, Y.51, S.72, Q.73, A.74, F.87, L.188, A.330, L.437 Ligands: SYN.9 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.20, B:P.25, B:V.26, B:F.42, B:T.49, B:A.74, B:F.87, B:L.188 Hydrogen bonds: B:Y.51, B:Q.73, B:A.74 Salt bridges: B:R.47 pi-Cation interactions: B:R.47

2 x SYN: ethenylbenzene(Non-covalent)

SYN.3: 6 residues within 4Å: Chain A: V.78, F.87, L.181, I.263, A.264 Ligands: D0L.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.78, A:F.87, A:F.87, A:L.181, A:I.263 SYN.9: 5 residues within 4Å: Chain B: V.78, F.87, I.263, A.264 Ligands: D0L.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.78, B:F.87, B:F.87, B:F.87, B:I.263, B:A.264

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: D.68, T.91, H.92, Y.334, K.336 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.336 Water bridges: A:Y.334, A:Y.334, A:Q.397 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:L.133, A:A.448, A:A.448, A:S.450 Water bridges: A:A.448 GOL.6: 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, A:Y.256 GOL.10: 7 residues within 4Å: Chain B: W.130, E.131, L.133, A.448, K.449, S.450, K.452 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.448, B:A.448, B:S.450

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional cytochrome P450/NADPH--P450 reductase

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