SMTL ID : 7wdg.1

Crystal structure of the P450 BM3 heme domain mutant F87L in complex with N-imidazolyl-hexanoyl-L-phenylalanine, phenol and hydroxylamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 26 residues within 4Å: Chain A: K.71, L.77, L.88, L.89, W.98, F.263, A.266, G.267, T.270, T.271, L.324, T.329, A.330, F.333, P.394, F.395, G.396, R.400, A.401, C.402, I.403, G.404, F.407, A.408 Ligands: HOA.2, IC6.4 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:L.88, A:L.89, A:F.263, A:A.266, A:L.324, A:F.395, A:I.403, A:F.407 Water bridges: A:K.71, A:K.71, A:H.102, A:S.334, A:S.334, A:S.334 Salt bridges: A:K.71, A:K.71, A:R.400 Metal complexes: A:C.402 HEM.8: 25 residues within 4Å: Chain B: K.71, L.77, L.88, L.89, W.98, F.263, A.266, G.267, T.270, T.271, L.324, T.329, A.330, F.333, P.394, F.395, G.396, R.400, A.401, C.402, I.403, G.404, A.408 Ligands: HOA.9, IC6.11 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:L.88, B:L.89, B:F.263, B:F.263, B:A.266, B:L.324, B:F.395, B:I.403 Water bridges: B:S.334, B:S.334, B:S.334, B:N.397, B:R.400 Salt bridges: B:K.71, B:R.400 Metal complexes: B:C.402

2 x HOA: HYDROXYAMINE(Non-covalent)

HOA.2: 4 residues within 4Å: Chain A: A.266, T.270 Ligands: HEM.1, IC6.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.266, A:T.270 Water bridges: A:T.270 HOA.9: 4 residues within 4Å: Chain B: A.266, T.270 Ligands: HEM.8, IC6.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.270

6 x IPH: PHENOL(Non-covalent)

IPH.3: 9 residues within 4Å: Chain A: V.80, L.89, I.265, A.266, E.269, L.439, T.440 Ligands: IC6.4, IC6.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.80, A:L.89, A:I.265, A:L.439, A:L.439 Hydrogen bonds: A:E.269 Water bridges: A:E.269, A:T.438 IPH.6: 6 residues within 4Å: Chain A: E.145, R.149, S.166, Q.171, P.172, H.173 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.149, A:P.172 Hydrogen bonds: A:S.166, A:H.173 IPH.7: 4 residues within 4Å: Chain A: V.310, K.311, G.317, T.413 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.413 Hydrogen bonds: A:V.310 Water bridges: A:K.311 IPH.10: 9 residues within 4Å: Chain B: V.80, L.89, I.265, A.266, E.269, L.439, T.440 Ligands: IC6.11, IC6.12 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.80, B:L.89, B:L.439, B:L.439 Hydrogen bonds: B:E.269, B:E.269 IPH.13: 7 residues within 4Å: Chain B: E.145, T.148, R.149, S.166, Q.171, P.172, H.173 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.148, B:P.172 IPH.14: 6 residues within 4Å: Chain B: V.310, K.311, L.313, G.317, L.409, T.413 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.413 Hydrogen bonds: B:H.410 Water bridges: B:Q.111, B:Q.406

4 x IC6: (2S)-2-(6-imidazol-1-ylhexanoylamino)-3-phenyl-propanoic acid(Non-covalent)

IC6.4: 15 residues within 4Å: Chain A: L.22, P.27, V.28, L.31, Y.53, A.76, L.89, M.187, A.330, A.332, L.439 Ligands: HEM.1, HOA.2, IPH.3, IC6.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.22, A:P.27, A:P.27, A:V.28, A:A.76 Hydrogen bonds: A:Y.53 Water bridges: A:S.74 IC6.5: 13 residues within 4Å: Chain A: L.22, F.44, R.49, Y.53, S.74, Q.75, A.76, A.330, A.332, M.356, L.439 Ligands: IPH.3, IC6.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.22, A:F.44, A:A.332 Hydrogen bonds: A:Y.53, A:Q.75, A:A.76 Salt bridges: A:R.49 pi-Cation interactions: A:R.49 IC6.11: 14 residues within 4Å: Chain B: P.27, V.28, L.31, Y.53, A.76, M.187, A.330, A.332, M.356, L.439 Ligands: HEM.8, HOA.9, IPH.10, IC6.12 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.27, B:P.27, B:V.28, B:L.31, B:A.76 Water bridges: B:S.74 IC6.12: 13 residues within 4Å: Chain B: L.22, F.44, R.49, Y.53, S.74, Q.75, A.76, A.330, A.332, M.356, L.439 Ligands: IPH.10, IC6.11 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.22, B:F.44, B:R.49, B:A.332 Hydrogen bonds: B:Q.75, B:A.76 Salt bridges: B:R.49 pi-Cation interactions: B:R.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X. et al., Engineering Cytochrome P450BM3 Enzymes for Direct Nitration of Unsaturated Hydrocarbons. Angew.Chem.Int.Ed.Engl. (2023)

Release Date

2022-12-28

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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