SMTL ID : 7wdd.1

Crystal structure of the P450 BM3 heme domain mutant F87K in complex with N-imidazolyl-hexanoyl-L-phenylalanine, styrene and hydroxylamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 27 residues within 4Å: Chain A: K.71, L.77, L.88, K.89, W.98, F.109, 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 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:L.88, A:K.89, A:F.109, A:F.263, A:F.263, A:A.266, A:L.274, 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, A:Q.399 Salt bridges: A:K.71, A:K.71, A:R.400 pi-Cation interactions: A:K.89 Metal complexes: A:C.402 HEM.5: 27 residues within 4Å: Chain B: K.71, L.77, L.88, K.89, W.98, F.109, I.155, F.263, A.266, G.267, T.270, T.271, 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.6, IC6.7 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:L.88, B:K.89, B:F.109, B:I.155, B:F.263, B:F.263, B:A.266, B:F.395, B:I.403, B:F.407 Water bridges: B:K.71, B:H.102, B:S.334, B:S.334, B:R.400, B:A.401 Salt bridges: B:K.71, B:K.71, B:R.400 pi-Cation interactions: B:K.89 Metal complexes: B:C.402

2 x HOA: HYDROXYAMINE(Non-covalent)

HOA.2: 5 residues within 4Å: Chain A: K.89, A.266, T.270 Ligands: HEM.1, IC6.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.89, A:K.89 Water bridges: A:T.270 HOA.6: 6 residues within 4Å: Chain B: K.89, A.266, T.270 Ligands: HEM.5, IC6.7, IC6.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.89, 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: 14 residues within 4Å: Chain A: P.27, V.28, Y.53, K.89, M.187, L.190, T.270, A.330, A.332, M.356, L.439 Ligands: HEM.1, HOA.2, IC6.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.27, A:P.27, A:V.28, A:L.190 Hydrogen bonds: A:Y.53, A:S.74 pi-Cation interactions: A:K.89 IC6.4: 13 residues within 4Å: Chain A: L.22, F.44, R.49, Y.53, S.74, Q.75, A.76, K.89, A.330, A.332, M.356, L.439 Ligands: IC6.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.22, A:F.44 Hydrogen bonds: A:Q.75, A:A.76 Salt bridges: A:R.49 pi-Cation interactions: A:R.49 IC6.7: 14 residues within 4Å: Chain B: P.27, V.28, Y.53, A.76, K.89, M.187, T.270, A.330, A.332, M.356, L.439 Ligands: HEM.5, HOA.6, IC6.8 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.27, B:P.27, B:V.28, B:A.76 Hydrogen bonds: B:K.89 Water bridges: B:S.74 pi-Cation interactions: B:K.89 IC6.8: 14 residues within 4Å: Chain B: L.22, F.44, R.49, Y.53, S.74, Q.75, A.76, K.89, A.330, A.332, M.356, L.439 Ligands: HOA.6, IC6.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.22, B:F.44, B:A.332 Hydrogen bonds: B:Q.75, B:A.76, B:K.89 Salt bridges: B:R.49 pi-Cation interactions: B:R.49

3 x SYN: ethenylbenzene(Non-covalent)

SYN.9: 4 residues within 4Å: Chain B: K.131, E.142, R.149, D.170 No protein-ligand interaction detected (PLIP) SYN.10: 4 residues within 4Å: Chain B: D.70, H.94, Y.336, K.338 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.70, B:H.94 pi-Cation interactions: B:H.94 SYN.11: 3 residues within 4Å: Chain B: R.81, G.85, D.86 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.81 pi-Cation interactions: B:R.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, Y. et al., Crystal structure of the P450 BM3 heme domain mutant F87A in complex with N-imidazolyl-hexanoyl-L-phenylalanine and hydroxylamine. To Be Published

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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