SMTL ID : 7wdh.1

Crystal structure of the P450 BM3 heme domain mutant F87A in complex with N-imidazolyl-hexanoyl-L-phenylalanine, phenol and hydroxylamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 29 residues within 4Å: Chain A: K.71, L.77, L.88, A.89, W.98, F.109, I.155, F.263, A.266, G.267, T.270, T.271, L.274, 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, IC6.3, IC6.4 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:L.88, A:A.89, A:F.109, A:I.155, A:F.263, A:F.263, A:A.266, A:L.274, A:F.395, A:I.403, A:F.407 Hydrogen bonds: A:R.400 Water bridges: A:K.71, A:H.102, A:S.334, A:S.334, A:S.334, A:R.400 Salt bridges: A:K.71, A:K.71, A:R.400 Metal complexes: A:C.402 HEM.9: 29 residues within 4Å: Chain B: K.71, L.77, L.88, A.89, W.98, F.109, I.155, F.263, A.266, G.267, T.270, T.271, L.274, 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.10, IC6.11, IC6.12 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:L.88, B:A.89, B:F.109, B:I.155, B:F.263, B:F.263, B:A.266, B:L.274, B:F.395, B:I.403, B:F.407 Hydrogen bonds: B:R.400 Water bridges: B:K.71, B:S.334, B:S.334, B:S.334, B:R.400 Salt bridges: B:K.71, B:K.71, B:R.400 Metal complexes: B:C.402

2 x HOA: HYDROXYAMINE(Non-covalent)

HOA.2: 5 residues within 4Å: Chain A: A.266, T.270 Ligands: HEM.1, IC6.3, IPH.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.270 Water bridges: A:T.270 HOA.10: 6 residues within 4Å: Chain B: A.266, T.270 Ligands: HEM.9, IC6.11, IC6.12, IPH.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.270, B:T.270 Water bridges: B:T.270

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

IC6.3: 15 residues within 4Å: Chain A: P.27, V.28, L.31, Y.53, A.76, M.187, A.330, A.332, M.356, L.439 Ligands: HEM.1, HOA.2, IC6.4, IPH.6, IPH.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.27, A:P.27, A:V.28, A:A.76 Hydrogen bonds: A:Y.53 Water bridges: A:S.74 IC6.4: 15 residues within 4Å: Chain A: L.22, F.44, R.49, Y.53, S.74, Q.75, A.76, L.190, A.330, A.332, M.356, L.439 Ligands: HEM.1, IC6.3, IPH.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.22, A:F.44, A:L.190, 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, T.270, A.330, A.332, M.356, L.439 Ligands: HEM.9, HOA.10, IC6.12, IPH.14 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.27, B:P.27, B:V.28, B:A.76 Water bridges: B:S.74 IC6.12: 15 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: HEM.9, HOA.10, IC6.11, IPH.14 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.22, B:F.44, B:A.332 Hydrogen bonds: B:Q.75, B:A.76 Salt bridges: B:R.49 pi-Cation interactions: B:R.49

7 x IPH: PHENOL(Non-covalent)

IPH.5: 7 residues within 4Å: Chain A: E.145, T.148, R.149, S.166, Q.171, P.172, H.173 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.148, A:R.149, A:P.172 Hydrogen bonds: A:H.173 IPH.6: 9 residues within 4Å: Chain A: Q.75, A.76, F.79, L.183, A.186, M.187, L.190, L.439 Ligands: IC6.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.76, A:F.79, A:L.183, A:A.186, A:L.190, A:L.439 Water bridges: A:Q.75, A:A.186 IPH.7: 8 residues within 4Å: Chain A: V.80, I.265, A.266, E.269, T.440 Ligands: HOA.2, IC6.3, IC6.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.80, A:I.265, A:A.266 Hydrogen bonds: A:E.269 Water bridges: A:E.269 IPH.8: 5 residues within 4Å: Chain A: I.368, W.369, R.380, A.386, P.388 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.369 Hydrogen bonds: A:R.380 Water bridges: A:R.377 IPH.13: 5 residues within 4Å: Chain B: N.321, F.381, P.384, I.387, F.392 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.381, B:P.384, B:I.387 Water bridges: B:F.392 pi-Stacking: B:F.392 IPH.14: 7 residues within 4Å: Chain B: I.265, A.266, E.269, T.440 Ligands: HOA.10, IC6.11, IC6.12 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.265, B:A.266 Hydrogen bonds: B:E.269, B:E.269 IPH.15: 8 residues within 4Å: Chain B: E.145, T.148, R.149, S.166, Q.171, P.172, H.173, I.176 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.148, B:R.149, B:I.176

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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