SMTL ID : 7y0p.1

Crystal structure of the P450 BM3 heme domain mutant F87A/T268V/A82T/I263L in complex with N-imidazolyl-hexanoyl-L-phenylalanine, p-cresol and hydroxylamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 30 residues within 4Å: Chain A: K.71, L.77, L.88, A.89, W.98, F.109, I.155, T.262, F.263, A.266, V.270, T.271, L.274, 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, IC6.3, IC6.4 27 PLIP interactions: 27 interactions with chain A, Hydrophobic interactions: A:A.89, A:F.109, A:I.155, A:T.262, A:F.263, A:F.263, A:F.263, A:A.266, A:V.270, A:L.274, A:L.324, A:F.395, A:F.395, A:I.403, A:F.407, A:A.408 Hydrogen bonds: A:R.400, A:R.400 Water bridges: A:K.71, A:K.71, 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.6: 29 residues within 4Å: Chain B: K.71, L.77, L.88, A.89, W.98, F.109, I.155, T.262, F.263, A.266, V.270, T.271, L.274, 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.7, IC6.9, IC6.10 27 PLIP interactions: 26 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:L.88, B:A.89, B:F.109, B:I.155, B:T.262, B:F.263, B:F.263, B:A.266, B:V.270, B:L.274, B:L.324, B:F.395, B:F.395, B:I.403, B:A.408 Hydrogen bonds: B:R.400, B:R.400 Water bridges: B:K.71, B:H.102, B:S.334, B:S.334, B:S.334 Salt bridges: B:K.71, B:K.71, B:R.400 Metal complexes: B:C.402, HOA.7

2 x HOA: HYDROXYAMINE(Non-covalent)

HOA.2: 5 residues within 4Å: Chain A: A.266, V.270 Ligands: HEM.1, IC6.3, IC6.4 No protein-ligand interaction detected (PLIP) HOA.7: 6 residues within 4Å: Chain B: A.266, V.270 Ligands: HEM.6, PCR.8, IC6.9, IC6.10 No protein-ligand interaction detected (PLIP)

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, A.89, M.187, L.190, A.330, A.332, M.356, L.439 Ligands: HEM.1, HOA.2, IC6.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.27, A:P.27, A:V.28, A:L.31, A:L.190, A:L.439 IC6.4: 15 residues within 4Å: Chain A: L.22, F.44, A.46, R.49, Y.53, S.74, Q.75, A.76, L.190, A.330, A.332, M.356 Ligands: HEM.1, HOA.2, IC6.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.22, A:F.44, A:A.46, A:R.49, A:Q.75, A:A.76, A:L.190, A:A.332 Hydrogen bonds: A:Q.75, A:A.76 Salt bridges: A:R.49 pi-Cation interactions: A:R.49 IC6.9: 16 residues within 4Å: Chain B: P.27, V.28, L.31, Y.53, A.76, A.89, M.187, L.190, A.330, A.332, M.356, L.439 Ligands: HEM.6, HOA.7, PCR.8, IC6.10 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.27, B:P.27, B:V.28, B:L.190, B:L.439, B:L.439 Hydrogen bonds: B:Y.53 IC6.10: 18 residues within 4Å: Chain B: L.22, F.44, A.46, R.49, Y.53, S.74, Q.75, A.76, L.77, L.190, A.330, A.332, M.356, L.439 Ligands: HEM.6, HOA.7, PCR.8, IC6.9 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.22, B:F.44, B:A.46, B:R.49, B:A.76, B:L.190, B:A.332 Hydrogen bonds: B:Y.53, B:Q.75, B:A.76 Salt bridges: B:R.49 pi-Cation interactions: B:R.49

3 x PCR: P-CRESOL(Non-covalent)

PCR.5: 6 residues within 4Å: Chain A: Y.162, H.173, F.175, L.217, I.221, L.264 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.175, A:L.217, A:I.221, A:I.221, A:L.264 Hydrogen bonds: A:Y.162 pi-Stacking: A:Y.162 PCR.8: 11 residues within 4Å: Chain B: A.89, L.183, L.265, A.266, E.269, V.270, L.439, T.440 Ligands: HOA.7, IC6.9, IC6.10 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.183, B:L.265, B:L.265, B:V.270, B:L.439, B:T.440 PCR.11: 9 residues within 4Å: Chain B: F.160, Y.162, F.164, H.173, F.175, L.217, V.218, I.221, L.264 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.160, B:F.164, B:F.175, B:V.218, B:I.221, B:L.264 Hydrogen bonds: B:H.173 pi-Stacking: B:Y.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, Y. et al., Crystal structure of the P450 BM3 heme domain mutant F87A/T268V/A82T/I263L in complex with N-imidazolyl-hexanoyl-L-phenylalanine, p-cresol and hydroxylamine. To Be Published

Release Date

2023-06-14

Peptides

Bifunctional cytochrome P450/NADPH--P450 reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Bifunctional cytochrome P450/NADPH--P450 reductase

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