SMTL ID : 6zi3.5 (5 other biounits)

Crystal structure of OleP-6DEB bound to L-rhamnose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

monomer

Ligands

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

HEM.1: 23 residues within 4Å: Chain A: V.93, L.94, H.101, R.105, F.112, I.157, A.244, G.245, T.248, S.249, Q.252, L.290, R.298, F.321, A.348, F.349, G.350, H.354, C.356, I.357, G.358, G.362 Ligands: DEB.2 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:F.112, A:I.157, A:L.290, A:F.321, A:I.357 Water bridges: A:F.296 Salt bridges: A:H.101, A:R.105, A:R.298, A:H.354 pi-Stacking: A:F.349 Metal complexes: A:C.356

1 x DEB: 6-DEOXYERYTHRONOLIDE B(Non-covalent)

DEB.2: 17 residues within 4Å: Chain A: M.83, F.84, L.94, M.178, L.179, I.243, A.244, T.248, V.291, S.295, F.296, L.396 Ligands: HEM.1, RAM.3, FMT.6, FMT.12, FMT.14 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:M.83, A:L.94, A:L.179, A:A.244, A:T.248, A:V.291, A:L.396

1 x RAM: alpha-L-rhamnopyranose(Non-covalent)

RAM.3: 12 residues within 4Å: Chain A: E.89, G.92, V.93, M.178, Q.193, N.236, S.240, I.243 Ligands: DEB.2, FMT.6, FMT.12, FMT.14 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.243 Hydrogen bonds: A:E.89, A:V.93, A:N.236, A:N.236, A:S.240, A:S.240 Water bridges: A:L.94

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

FMT.4: 3 residues within 4Å: Chain A: F.349, H.355, R.363 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.355, A:R.363, A:R.363 FMT.5: 4 residues within 4Å: Chain A: T.182, R.183, Q.393, G.394 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.182 FMT.6: 7 residues within 4Å: Chain A: E.89, G.92, A.95, F.296 Ligands: DEB.2, RAM.3, FMT.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.89, A:E.89 Water bridges: A:L.94 FMT.7: 1 residues within 4Å: Chain A: R.106 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.106 FMT.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FMT.9: 2 residues within 4Å: Chain A: A.73, Q.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.233 Water bridges: A:D.100 FMT.10: 4 residues within 4Å: Chain A: D.97, P.98, P.99, D.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.98, A:D.100, A:D.100 FMT.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FMT.12: 6 residues within 4Å: Chain A: T.86, E.89, Q.193 Ligands: DEB.2, RAM.3, FMT.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.86, A:E.89 FMT.13: 3 residues within 4Å: Chain A: S.130, L.131, D.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.130 FMT.14: 7 residues within 4Å: Chain A: M.178, N.236, V.239, S.240, I.243 Ligands: DEB.2, RAM.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.236, A:N.236

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

NA.15: 4 residues within 4Å: Chain A: R.82, F.84, F.296, V.297 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.297 Water bridges: A:P.81, A:S.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parisi, G. et al., Dissecting the Cytochrome P450 OleP Substrate Specificity: Evidence for a Preferential Substrate. Biomolecules (2020)

Release Date

2020-10-21

Peptides

Cytochrome P-450: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

Cytochrome P-450

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