SMTL ID : 8qyi.3 (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 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: 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: 16 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.5, FMT.15 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.170, A:I.234, A:I.234, A:A.235, A:T.239 Hydrogen bonds: A:N.227, A:G.285 Water bridges: A:F.287

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

FMT.3: 3 residues within 4Å: Chain A: D.120, D.124, R.367 Ligand excluded by PLIP FMT.4: 7 residues within 4Å: Chain A: S.11, P.13, D.17, L.18, D.19, Y.22, R.389 Ligand excluded by PLIP FMT.5: 5 residues within 4Å: Chain A: F.75, L.85, F.287 Ligands: 4OA.2, FMT.15 Ligand excluded by PLIP FMT.6: 3 residues within 4Å: Chain A: L.267, A.270, F.330 Ligand excluded by PLIP FMT.7: 2 residues within 4Å: Chain A: P.155, Q.197 Ligand excluded by PLIP FMT.8: 4 residues within 4Å: Chain A: R.257, L.328, D.329, F.330 Ligand excluded by PLIP FMT.9: 2 residues within 4Å: Chain A: E.296, T.301 Ligand excluded by PLIP FMT.10: 3 residues within 4Å: Chain A: A.15, H.249, V.377 Ligand excluded by PLIP FMT.11: 3 residues within 4Å: Chain A: E.320, V.321 Ligands: FMT.22 Ligand excluded by PLIP FMT.12: 3 residues within 4Å: Chain A: F.340, H.346, R.354 Ligand excluded by PLIP FMT.13: 3 residues within 4Å: Chain A: R.96, H.346, C.347 Ligand excluded by PLIP FMT.14: 1 residues within 4Å: Chain A: D.160 Ligand excluded by PLIP FMT.15: 6 residues within 4Å: Chain A: E.80, G.83, L.85, F.287 Ligands: 4OA.2, FMT.5 Ligand excluded by PLIP FMT.16: 2 residues within 4Å: Chain A: R.182, Q.185 Ligand excluded by PLIP FMT.17: 3 residues within 4Å: Chain A: R.48, S.50, S.298 Ligand excluded by PLIP FMT.18: 4 residues within 4Å: Chain A: D.28, E.29, P.30, T.299 Ligand excluded by PLIP FMT.19: 3 residues within 4Å: Chain A: T.173, R.174, G.385 Ligand excluded by PLIP FMT.20: 3 residues within 4Å: Chain A: A.146, E.150, L.156 Ligand excluded by PLIP FMT.21: 3 residues within 4Å: Chain A: M.49, R.53, V.321 Ligand excluded by PLIP FMT.22: 4 residues within 4Å: Chain A: V.321, F.322, D.323 Ligands: FMT.11 Ligand excluded by PLIP FMT.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP FMT.24: 7 residues within 4Å: Chain A: V.136, V.141, R.163, V.241, K.383, L.391, E.392 Ligand excluded by PLIP FMT.25: 3 residues within 4Å: Chain A: R.97, G.100, K.101 Ligand excluded by PLIP FMT.26: 1 residues within 4Å: Chain A: A.105 Ligand excluded by PLIP

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

NA.27: 3 residues within 4Å: Chain A: 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
C

Cytochrome P-450

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