SMTL ID : 8qyi.4 (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, A.235, G.236, T.239, S.240, Q.243, L.281, F.287, R.289, F.312, A.339, F.340, G.341, H.345, C.347, I.348, G.349, G.353 Ligands: 4OA.2 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:F.103, A:A.235, A:L.281, A:F.340, A:I.348 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: 17 residues within 4Å: Chain A: E.80, G.83, M.169, L.170, N.227, S.231, I.234, A.235, T.239, V.282, S.286, F.312, I.388 Ligands: HEM.1, FMT.3, FMT.6, FMT.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.170, A:I.234, A:T.239, A:V.282 Hydrogen bonds: A:N.227 Water bridges: A:F.287

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

FMT.3: 8 residues within 4Å: Chain A: M.74, F.75, V.282, A.284, G.285, S.286, F.287 Ligands: 4OA.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.285 Water bridges: A:M.74, A:A.284, A:F.287 FMT.4: 1 residues within 4Å: Chain A: T.299 No protein-ligand interaction detected (PLIP) FMT.5: 5 residues within 4Å: Chain A: A.23, R.26, R.27, R.317, E.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.26, A:E.319 FMT.6: 4 residues within 4Å: Chain A: F.75, F.287 Ligands: 4OA.2, FMT.7 No protein-ligand interaction detected (PLIP) FMT.7: 7 residues within 4Å: Chain A: P.79, E.80, G.83, A.86, F.287 Ligands: 4OA.2, FMT.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.80, A:A.86 FMT.8: 3 residues within 4Å: Chain A: M.49, R.53, V.321 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.53 FMT.9: 3 residues within 4Å: Chain A: R.257, L.328, F.330 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.330 FMT.10: 4 residues within 4Å: Chain A: E.29, S.32, R.33, W.44 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.29, A:R.33 FMT.11: 4 residues within 4Å: Chain A: V.141, R.159, D.160, R.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.159, A:R.163 FMT.12: 6 residues within 4Å: Chain A: P.13, A.15, W.382, K.383, R.389, G.390 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.15, A:K.383, A:G.390 FMT.13: 4 residues within 4Å: Chain A: V.5, P.6, A.7, R.35 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.35 FMT.14: 5 residues within 4Å: Chain A: V.282, G.285, H.311, F.312, A.313 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.311, A:F.312, A:A.313 Water bridges: A:V.282 FMT.15: 4 residues within 4Å: Chain A: D.329, H.331, R.332, E.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.329, A:E.333

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

NA.16: 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:P.72

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
D

Cytochrome P-450

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