SMTL ID : 8qyi.1 (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: 23 residues within 4Å: Chain A: V.84, L.85, H.92, R.96, F.103, I.148, A.235, G.236, T.239, Q.243, L.281, F.287, R.289, F.312, A.339, F.340, G.341, H.345, C.347, I.348, G.349, L.357 Ligands: 4OA.2 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:V.84, A:F.103, A:I.148, A:A.235, A:Q.243, 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 Metal complexes: A:C.347

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

4OA.2: 14 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, I.388 Ligands: HEM.1, FMT.15 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.170, A:I.234, A:I.234, A:T.239, A:V.282 Hydrogen bonds: A:N.227, A:G.285 Water bridges: A:S.231, A:F.287, A:F.287

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

FMT.3: 3 residues within 4Å: Chain A: T.173, R.174, G.385 Ligand excluded by PLIP FMT.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP FMT.5: 4 residues within 4Å: Chain A: R.26, R.317, D.318, E.319 Ligand excluded by PLIP FMT.6: 2 residues within 4Å: Chain A: P.90, R.94 Ligand excluded by PLIP FMT.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP FMT.8: 3 residues within 4Å: Chain A: M.49, S.50, R.53 Ligand excluded by PLIP FMT.9: 1 residues within 4Å: Chain A: P.202 Ligand excluded by PLIP FMT.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP FMT.11: 2 residues within 4Å: Chain A: S.121, D.125 Ligand excluded by PLIP FMT.12: 6 residues within 4Å: Chain A: R.198, R.199, P.202, G.208, A.211, L.212 Ligand excluded by PLIP FMT.13: 1 residues within 4Å: Chain A: T.299 Ligand excluded by PLIP FMT.14: 4 residues within 4Å: Chain A: R.257, L.328, D.329, F.330 Ligand excluded by PLIP FMT.15: 6 residues within 4Å: Chain A: E.80, G.83, A.86, F.287 Ligands: 4OA.2, FMT.22 Ligand excluded by PLIP FMT.16: 4 residues within 4Å: Chain A: A.105, E.109, Q.351, R.354 Ligand excluded by PLIP FMT.17: 6 residues within 4Å: Chain A: F.75, P.76, T.77, M.169, S.171, I.180 Ligand excluded by PLIP FMT.18: 6 residues within 4Å: Chain A: D.17, L.18, D.19, Y.22, S.283, R.389 Ligand excluded by PLIP FMT.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP FMT.20: 2 residues within 4Å: Chain A: A.178, E.179 Ligand excluded by PLIP FMT.21: 4 residues within 4Å: Chain A: A.270, E.273, E.274, N.335 Ligand excluded by PLIP FMT.22: 4 residues within 4Å: Chain A: F.75, L.85, F.287 Ligands: FMT.15 Ligand excluded by PLIP FMT.23: 3 residues within 4Å: Chain A: H.342, G.343, H.346 Ligand excluded by PLIP FMT.24: 5 residues within 4Å: Chain A: S.59, F.61, S.62, D.88, P.89 Ligand excluded by PLIP

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

NA.25: 4 residues within 4Å: Chain A: R.73, F.75, F.287, V.288 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.288 Water bridges: A:S.286

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
A

Cytochrome P-450

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