SMTL ID : 8jc4.1

Crystal structure of the P450 BM3 heme domain mutant F87A-T268V in complex with Pyd-Pid-Phe and hydroxylamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

homo-dimer

Ligands

2 x HOA: HYDROXYAMINE(Non-covalent)

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

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

HEM.2: 27 residues within 4Å: Chain A: K.71, L.77, L.88, A.89, W.98, F.109, F.263, A.266, G.267, V.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.1, UCH.3 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:L.88, A:A.89, A:F.109, A:F.109, A:F.263, A:F.263, A:A.266, A:V.270, A:L.274, A:F.395, A:I.403, A:F.407 Hydrogen bonds: A:R.400 Salt bridges: A:K.71, A:K.71, A:R.400 Metal complexes: A:C.402 HEM.8: 26 residues within 4Å: Chain B: K.71, L.77, L.88, A.89, W.98, F.109, F.263, A.266, V.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.7, UCH.9 20 PLIP interactions: 19 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:L.88, B:A.89, B:F.109, B:F.263, B:F.263, B:A.266, B:V.270, B:L.274, B:F.395, B:I.403, B:F.407 Hydrogen bonds: B:R.400 Water bridges: 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

4 x UCH: 1-pyridin-4-ylpiperidine-4-carboxylic acid(Non-covalent)

UCH.3: 11 residues within 4Å: Chain A: S.74, L.77, A.330, P.331, A.332, L.439 Ligands: HOA.1, HEM.2, PHE.4, UCH.5, PHE.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.330 UCH.5: 9 residues within 4Å: Chain A: L.31, Y.53, A.76, P.331, A.332, L.439 Ligands: UCH.3, PHE.4, PHE.6 4 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain A Hydrophobic interactions: F.4, F.4, A:A.332 Hydrogen bonds: A:Y.53 UCH.9: 11 residues within 4Å: Chain B: S.74, L.77, A.330, P.331, A.332, L.439 Ligands: HOA.7, HEM.8, PHE.10, UCH.11, PHE.12 No protein-ligand interaction detected (PLIP) UCH.11: 9 residues within 4Å: Chain B: Y.53, A.76, P.331, A.332, M.356, L.439 Ligands: UCH.9, PHE.10, PHE.12 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain B Hydrophobic interactions: F.10, B:A.332

4 x PHE: PHENYLALANINE(Non-covalent)

PHE.4: 11 residues within 4Å: Chain A: L.22, P.27, V.28, L.31, Y.53, M.187, L.190, M.356 Ligands: UCH.3, UCH.5, PHE.6 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.22, A:P.27, A:P.27, A:V.28, A:L.190, F.6 Hydrogen bonds: A:Y.53 PHE.6: 12 residues within 4Å: Chain A: L.22, F.44, R.49, T.51, Y.53, S.74, Q.75, A.76, L.190 Ligands: UCH.3, PHE.4, UCH.5 9 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain A Hydrophobic interactions: F.4, A:L.22, A:F.44, A:R.49, A:T.51 Hydrogen bonds: A:Q.75, A:A.76 Salt bridges: A:R.49 pi-Cation interactions: A:R.49 PHE.10: 11 residues within 4Å: Chain B: L.22, P.27, V.28, L.31, Y.53, M.187, L.190, M.356 Ligands: UCH.9, UCH.11, PHE.12 8 PLIP interactions: 6 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:L.22, B:P.27, B:P.27, B:V.28, B:L.31, B:L.190, F.12 Hydrogen bonds: F.12 PHE.12: 10 residues within 4Å: Chain B: L.22, R.49, Y.53, S.74, Q.75, A.76, L.190 Ligands: UCH.9, PHE.10, UCH.11 11 PLIP interactions: 8 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:L.22, B:R.49, B:Q.75, B:L.190, F.10 Hydrogen bonds: B:Q.75, B:A.76, F.10, F.12 Salt bridges: B:R.49 pi-Cation interactions: B:R.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qin, X. et al., C(sp3)-H hydroxylation of Broad-Spectrum Alkanes Catalyzed by an Artificial P450 Peroxygenase Driven by omega-Pyridyl Fatty Acyl Amino Acids. Mol Catal (2023)

Release Date

2023-12-27

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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