SMTL ID : 7wy4.1 (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.262, A.265, G.266, T.269, T.270, L.323, T.328, A.329, F.332, P.393, F.394, G.395, R.399, A.400, C.401, I.402, G.403, F.406, A.407 Ligands: SYN.3 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:L.87, A:A.88, A:F.262, A:A.265, A:T.269, A:L.323, A:F.394, A:I.402, A:F.406 Hydrogen bonds: A:R.399 Water bridges: A:K.70, A:K.70, A:S.73, 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: 14 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.331, M.355, L.438 Ligands: GOL.5 11 PLIP interactions: 11 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:L.438 Hydrogen bonds: A:Y.52, A:Q.74, A:A.75 pi-Cation interactions: A:R.48

1 x SYN: ethenylbenzene(Non-covalent)

SYN.3: 6 residues within 4Å: Chain A: L.76, A.88, T.261, I.264, A.265 Ligands: HEM.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.76, A:A.88, A:T.261, A:I.264, A:I.264, A:A.265

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

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

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: T.23, D.24, P.26, M.186, Q.190, E.436, T.437 Ligands: D0L.2, GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.23 Water bridges: A:Q.190, A:T.437 GOL.6: 6 residues within 4Å: Chain A: I.367, W.368, R.379, N.382, A.385, I.386 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.367, A:R.379 Water bridges: A:R.376, A:N.382 GOL.7: 6 residues within 4Å: Chain A: N.22, T.23, D.24, N.187, Q.190 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.23, A:Q.190 GOL.8: 4 residues within 4Å: Chain A: D.69, H.93, Y.335, K.337 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.337, A:K.337 Water bridges: A:E.65 GOL.9: 2 residues within 4Å: Chain A: D.64, Q.388 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.64, A:Q.388, A:Q.388 Water bridges: A:C.63, A:C.63, A:D.64, A:E.65 GOL.10: 7 residues within 4Å: Chain A: H.101, L.105, G.397, Q.398, A.400, C.401, I.402 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.398, A:C.401 GOL.11: 8 residues within 4Å: Chain A: W.131, E.132, L.134, N.135, A.136, A.449, K.450, S.451 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.132, A:L.134, A:N.135, A:S.451 Water bridges: A:S.451 GOL.12: 3 residues within 4Å: Chain A: W.91, Y.335, G.351 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.350 GOL.13: 2 residues within 4Å: Chain A: E.132, R.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.132, A:R.133 Water bridges: A:K.453 GOL.14: 7 residues within 4Å: Chain A: R.48, N.71, L.72, S.73, Q.74, K.77, E.353 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.71, A:Q.74, A:E.353 Water bridges: A:V.49, A:K.77

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
A

Bifunctional cytochrome P450/NADPH--P450 reductase

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