SMTL ID : 8qyi.6 (5 other biounits)

OleP in complex with lithocholic acid in high salt crystallization conditions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

HEM.1: 24 residues within 4Å: Chain A: V.84, L.85, H.92, R.96, F.103, L.232, A.235, G.236, T.239, Q.243, L.276, L.281, R.289, F.312, A.339, F.340, G.341, H.345, C.347, I.348, G.349, G.353, L.357 Ligands: 4OA.2 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:F.103, A:L.232, A:A.235, A:Q.243, A:L.276, A:L.281, A:F.340, A:I.348, A:L.357 Hydrogen bonds: A:F.287 Salt bridges: A:H.92, A:R.96, A:R.289, A:H.345 pi-Stacking: A:F.340 Metal complexes: A:C.347

1 x 4OA: (3beta,5beta,14beta,17alpha)-3-hydroxycholan-24-oic acid(Non-covalent)

4OA.2: 16 residues within 4Å: Chain A: E.80, G.83, L.170, N.227, S.231, I.234, A.235, T.239, V.282, S.286, F.312, L.387, I.388 Ligands: HEM.1, FMT.4, FMT.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.170, A:I.234, A:T.239, A:L.387 Hydrogen bonds: A:N.227, A:G.285, A:F.287 Water bridges: A:V.84

11 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 3 residues within 4Å: Chain A: R.96, G.100, I.348 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.96 FMT.4: 4 residues within 4Å: Chain A: F.75, F.287 Ligands: 4OA.2, FMT.9 No protein-ligand interaction detected (PLIP) FMT.5: 4 residues within 4Å: Chain A: M.74, S.172, S.283, A.284 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.283 FMT.6: 3 residues within 4Å: Chain A: F.340, H.346, R.354 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.346, A:R.354, A:R.354 FMT.7: 3 residues within 4Å: Chain A: R.48, S.50, S.298 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.48, A:S.50 Water bridges: A:S.298 FMT.8: 2 residues within 4Å: Chain A: T.221, E.224 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.91, A:D.91, A:T.221 FMT.9: 7 residues within 4Å: Chain A: E.80, G.83, L.85, A.86, F.287 Ligands: 4OA.2, FMT.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.80, A:E.80 Water bridges: A:L.85 FMT.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FMT.11: 2 residues within 4Å: Chain A: T.104, A.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.105 Water bridges: A:R.106 FMT.12: 3 residues within 4Å: Chain A: K.101, T.104, R.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.104, A:R.106 Water bridges: A:R.106 FMT.13: 1 residues within 4Å: Chain A: T.104 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.14: 4 residues within 4Å: Chain A: R.73, F.75, F.287, V.288 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Costanzo, A. et al., Binding of steroid substrates reveals the key to the productive transition of the cytochrome P450 OleP. Structure (2024)

Release Date

2024-07-03

Peptides

Cytochrome P-450: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

Cytochrome P-450

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