SMTL ID : 6l1b.1 (1 other biounit)

Crystal Structure of P450BM3 with N-(3-cyclopentylpropanoyl)-L-pipecolyl-L-phenylalanine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 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, F.88, W.97, F.108, I.154, F.262, 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: DMS.2 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:L.87, A:F.88, A:F.88, A:F.108, A:I.154, A:F.262, A:A.265, 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:S.333, A:S.333, A:S.333 Salt bridges: A:K.70, A:R.399 Metal complexes: A:C.401

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 4 residues within 4Å: Chain A: F.88, A.265, T.269 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.88

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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:L.72, A:Q.74 Water bridges: A:K.77, A:K.77 GOL.4: 5 residues within 4Å: Chain A: D.69, T.92, H.93, Y.335, K.337 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.335, A:K.337 Water bridges: A:D.69 GOL.5: 5 residues within 4Å: Chain A: K.392, G.395, N.396, G.397, Q.404 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.392, A:K.392, A:G.397, A:Q.404, A:Q.404 GOL.6: 2 residues within 4Å: Chain A: D.423, F.424 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.423, A:F.424, A:K.452 GOL.7: 3 residues within 4Å: Chain A: H.286, Q.289, K.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.290

1 x YIC: (2S)-2-[[(2S)-1-(3-cyclopentylpropanoyl)piperidin-2-yl]carbonylamino]-3-phenyl-propanoic acid(Non-covalent)

YIC.8: 18 residues within 4Å: Chain A: L.21, P.26, V.27, L.30, F.43, R.48, Y.52, S.73, Q.74, A.75, F.88, M.186, L.189, A.329, P.330, A.331, M.355, L.438 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.21, A:P.26, A:V.27, A:L.30, A:F.43, A:A.75, A:F.88, A:A.329, A:L.438 Hydrogen bonds: A:Y.52, A:Q.74, A:A.75 Water bridges: A:S.73 Salt bridges: A:R.48 pi-Cation interactions: A:R.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yonemura, K. et al., Systematic Evolution of Decoy Molecules for the Highly Efficient Hydroxylation of Benzene and Small Alkanes Catalyzed by Wild-Type Cytochrome P450BM3. Acs Catalysis (2020)

Release Date

2020-09-30

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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