SMTL ID : 8gue.2 (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: 27 residues within 4Å: Chain A: K.72, M.92, L.93, H.100, R.104, F.111, A.243, G.244, T.247, T.248, L.284, P.289, V.290, 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 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:L.93, A:L.93, A:F.111, A:A.243, A:L.284, A:P.289, A:V.290, A:F.347, 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: 16 residues within 4Å: Chain A: W.74, E.85, L.93, F.178, V.179, M.191, X.238, I.239, V.242, A.243, T.247, T.294, Y.295, N.392, I.395 Ligands: HEM.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.93, A:F.178, A:I.239, A:A.243, A:T.247, A:I.395 Salt bridges: A:E.85

4 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: 6 residues within 4Å: Chain A: R.36, G.57, Y.58, D.59, R.60, T.325 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.58, A:D.59, A:D.59, A:D.59, A:R.60 Salt bridges: A:R.60 SO4.5: 2 residues within 4Å: Chain A: R.114, R.115 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.115 SO4.7: 3 residues within 4Å: Chain A: A.33, R.36, P.326 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.36, A:R.36, A:R.324 Salt bridges: A:R.36

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 3 residues within 4Å: Chain A: T.112, M.113, R.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.113, A:R.114 EDO.8: 2 residues within 4Å: Chain A: T.82, E.83 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.83, A:E.83

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

PEG.9: 3 residues within 4Å: Chain A: P.98, R.99, R.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.102 Water bridges: A:R.227

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
B

Cytochrome P450 monooxygenase PikC

Related Entries With Identical Sequence