SMTL ID : 7wy4.2 (1 other biounit)

Structure of the CYP102A1 F87A Haem Domain with N-Enanthyl-L-Prolyl-L-Phenylalanine in complex with Styrene

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

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

HEM.1: 25 residues within 4Å: Chain A: K.70, L.76, L.87, A.88, W.97, F.108, I.154, T.261, A.265, 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 Ligands: SYN.3 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:L.87, A:A.88, A:F.108, A:I.154, A:T.261, A:A.265, A:T.269, A:L.273, A:A.329, A:F.394, A:I.402 Hydrogen bonds: A:R.399 Water bridges: A:K.70, A:K.70, A:H.101, A:S.333, A:S.333, A:S.333, A:S.333 Salt bridges: A:K.70, A:R.399 Metal complexes: A:C.401

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

D0L.2: 16 residues within 4Å: Chain A: L.21, P.26, L.30, R.48, Y.52, S.73, Q.74, A.75, M.186, L.189, A.329, A.331, M.355, L.438 Ligands: SYN.3, GOL.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.21, A:P.26, A:L.30, A:Q.74, A:A.75, A:L.189, A:A.329 Hydrogen bonds: A:Q.74, A:A.75 pi-Cation interactions: A:R.48

1 x SYN: ethenylbenzene(Non-covalent)

SYN.3: 5 residues within 4Å: Chain A: L.76, A.88, I.264 Ligands: HEM.1, D0L.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.76, A:A.88, A:I.264

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: T.11, G.13 Ligand excluded by PLIP

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: K.392, F.394, G.395, N.396, G.397, Q.404 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.392, A:K.392, A:G.397, A:Q.404, A:Q.404 Water bridges: A:H.389, A:H.389, A:N.396 GOL.6: 8 residues within 4Å: Chain A: T.23, D.24, P.26, M.186, Q.190, E.436, T.437 Ligands: D0L.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.23 Water bridges: A:D.183, A:E.436, A:T.437 GOL.7: 2 residues within 4Å: Chain A: E.132, R.133 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.133 GOL.8: 5 residues within 4Å: Chain A: I.367, W.368, R.379, A.385, P.387 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.379 GOL.9: 4 residues within 4Å: Chain A: D.69, H.93, Y.335, K.337 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.337 Water bridges: A:E.65, A:Y.335, A:Q.398, A:Q.398 GOL.10: 5 residues within 4Å: Chain A: R.80, G.84, D.85, E.253, Y.257 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.80, A:E.253 Water bridges: A:R.80, A:N.96 GOL.11: 2 residues within 4Å: Chain A: E.138, H.139 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.139, A:E.141 Water bridges: A:H.139, A:E.141, A:E.141 GOL.12: 5 residues within 4Å: Chain A: Q.289, A.292, E.293, A.296, K.452 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.289, A:K.452, A:K.452 Water bridges: A:E.293, A:E.293 GOL.13: 3 residues within 4Å: Chain A: V.49, G.351, E.353 4 PLIP interactions: 4 interactions with chain A Water bridges: A:V.49, A:R.51, A:G.351, A:E.353

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, K. et al., A Compound I Mimic Reveals the Transient Active Species of a Cytochrome P450 Enzyme: Insight into the Stereoselectivity of P450-Catalysed Oxidations. Angew.Chem.Int.Ed.Engl. (2023)

Release Date

2023-01-04

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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