SMTL ID : 8gue.1 (1 other biounit)

Crystal Structure of narbomycin-bound cytochrome P450 PikC with the unnatural amino acid p-Acetyl-L-Phenylalanine incorporated at position 238

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

HEM.1: 26 residues within 4Å: Chain A: K.72, M.92, L.93, H.100, R.104, L.240, A.243, G.244, T.247, T.248, L.284, P.289, A.293, T.294, R.296, A.346, F.347, G.348, I.351, H.352, C.354, I.355, G.356, L.359, A.360 Ligands: NRB.2 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:L.93, A:L.93, A:A.243, A:L.284, A:P.289, A:F.347, A:I.355, A:L.359 Hydrogen bonds: A:T.294, A:T.294 Salt bridges: A:K.72, A:H.100, A:R.104, A:R.296, A:H.352 pi-Stacking: A:F.347 Metal complexes: A:C.354

1 x NRB: NARBOMYCIN(Non-covalent)

NRB.2: 17 residues within 4Å: Chain A: W.74, E.85, L.93, F.178, M.191, X.238, I.239, V.242, A.243, E.246, T.247, V.290, T.294, Y.295, N.392, I.395 Ligands: HEM.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.178, A:F.178, A:I.239, A:V.242, A:A.243, A:T.247, A:V.290, A:I.395 Salt bridges: A:E.85

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: R.62, H.349 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.62, A:H.349 SO4.4: 3 residues within 4Å: Chain A: D.224, G.225, S.226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.224, A:G.225, A:S.226 SO4.5: 3 residues within 4Å: Chain A: S.383, P.384, G.385 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.385 Water bridges: A:S.383, A:S.383 SO4.6: 3 residues within 4Å: Chain A: A.33, R.36, P.326 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.36, A:R.36 Salt bridges: A:R.36 SO4.7: 3 residues within 4Å: Chain A: R.120, L.276, R.369 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.120, A:R.369 SO4.8: 1 residues within 4Å: Chain A: R.115 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.115 SO4.9: 3 residues within 4Å: Chain A: R.75, R.99 Ligands: PEG.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.232 Water bridges: A:H.90, A:R.99, A:R.99 Salt bridges: A:R.75, A:R.99

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.10: 6 residues within 4Å: Chain A: R.36, G.57, Y.58, D.59, R.60, T.325 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.58, A:D.59, A:R.60

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 4 residues within 4Å: Chain A: P.98, R.99, R.102 Ligands: SO4.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, Y. et al., Unnatural activities and mechanistic insights of cytochrome P450 PikC gained from site-specific mutagenesis by non-canonical amino acids. Nat Commun (2023)

Release Date

2023-02-15

Peptides

Cytochrome P450 monooxygenase PikC: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytochrome P450 monooxygenase PikC

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