SMTL ID : 8tdp.1

Time-resolved SFX-XFEL crystal structure of CYP121 bound with cYY reacted with peracetic acid for 200 milliseconds

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: S.11, R.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.11, A:S.11 Water bridges: A:A.12 SO4.2: 5 residues within 4Å: Chain A: R.57, S.60, M.61, K.62, H.342 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.61, A:K.62 Salt bridges: A:R.57, A:K.62, A:H.342 SO4.3: 5 residues within 4Å: Chain A: P.329, N.330, P.331, T.332, S.333 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.332, A:T.332, A:T.332 SO4.7: 5 residues within 4Å: Chain A: R.133, N.134, F.160, S.164, R.380 6 PLIP interactions: 6 interactions with chain A Water bridges: A:N.134, A:S.164, A:R.380, A:R.380 Salt bridges: A:R.133, A:R.380 SO4.8: 1 residues within 4Å: Chain A: S.218 No protein-ligand interaction detected (PLIP)

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

HEM.4: 21 residues within 4Å: Chain A: M.61, M.85, H.145, F.229, A.232, G.233, S.236, T.237, F.240, F.279, L.283, R.285, A.336, F.337, G.338, H.342, C.344, P.345, G.346 Ligands: YTT.5, PEO.6 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:F.229, A:F.229, A:A.232, A:F.240, A:F.279, A:F.279, A:F.337, A:P.345 Water bridges: A:M.85, A:R.94, A:R.94 Salt bridges: A:R.285, A:H.342 Metal complexes: A:C.344

1 x YTT: (3S,6S)-3,6-bis(4-hydroxybenzyl)piperazine-2,5-dione(Non-covalent)

YTT.5: 11 residues within 4Å: Chain A: M.61, V.77, V.81, V.82, N.84, A.166, F.167, T.228, R.385 Ligands: HEM.4, PEO.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.77, A:T.228 Hydrogen bonds: A:N.84, A:R.385, A:R.385 Water bridges: A:T.76, A:T.76, A:V.82, A:Q.384 pi-Stacking: A:F.167

1 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.6: 5 residues within 4Å: Chain A: A.232, S.236, R.385 Ligands: HEM.4, YTT.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.236, A:S.236, A:R.385

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, R.C. et al., In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121. J.Am.Chem.Soc. (2023)

Release Date

2023-11-22

Peptides

Mycocyclosin synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mycocyclosin synthase

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