SMTL ID : 9kt5.2 (1 other biounit)

Synchrotron X-ray crystal structure of oxygen-bound F87A/F393H P450BM3 with decoy C7ProPhe (N-enanthyl-L-prolyl-L-phenylalanine) and substrate styrene at 2 MGy X-ray dose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE

HEM.1: 26 residues within 4Å: Chain A: K.70, L.76, L.87, A.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, H.394, G.395, R.399, A.400, C.401, I.402, G.403, A.407 Ligands: SYN.2, OXY.3 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:L.87, A:A.88, A:F.108, A:F.262, A:F.262, A:A.265, A:L.273, A:A.329, A:I.402 Water bridges: A:K.70, A:K.70, A:S.333, A:S.333, A:S.333, A:R.399 Salt bridges: A:K.70, A:R.399 pi-Cation interactions: A:H.394 Metal complexes: A:C.401

1 x SYN: ethenylbenzene

SYN.2: 7 residues within 4Å: Chain A: A.88, I.264, A.265, T.439 Ligands: HEM.1, OXY.3, D0L.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.88, A:I.264, A:A.265, A:T.439

1 x OXY: OXYGEN MOLECULE

OXY.3: 4 residues within 4Å: Chain A: A.265, T.269 Ligands: HEM.1, SYN.2 No protein-ligand interaction detected (PLIP)

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

D0L.4: 16 residues within 4Å: Chain A: L.21, P.26, V.27, L.30, F.43, R.48, T.50, Y.52, S.73, Q.74, A.75, L.76, L.189, A.331, M.355 Ligands: SYN.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.21, A:P.26, A:V.27, A:F.43, A:T.50, A:A.75, A:L.76, A:L.189 Hydrogen bonds: A:Y.52, A:Q.74, A:A.75 Salt bridges: A:R.48 pi-Cation interactions: A:R.48

3 x GOL: GLYCEROL

GOL.5: 5 residues within 4Å: Chain A: D.69, T.92, H.93, Y.335, K.337 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.69, A:Y.335, A:K.337 Water bridges: A:K.337, A:Q.398 GOL.6: 6 residues within 4Å: Chain A: K.392, G.395, N.396, G.397, A.400, Q.404 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.392, A:K.392, A:G.397, A:Q.404 Water bridges: A:N.396, A:N.396 GOL.7: 5 residues within 4Å: Chain A: V.309, K.310, L.312, G.316, T.412 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.310, A:K.310, A:L.312

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagao, S. et al., XFEL crystallography reveals catalytic cycle dynamics during non-native substrate oxidation by cytochrome P450BM3. Commun Chem (2025)

Release Date

2025-03-26

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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