9IFD | pdb_00009ifd

OleP triple mutant F84Q/S240A/V291G in complex with LCA

PDB DOI: https://doi.org/10.2210/pdb9IFD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces antibioticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-02-18 Released: 2026-09-02
Deposition Author(s): Montemiglio, L.C., Costanzo, A., Fata, F., Freda, I., Demitri, N., Savino, C., Vallone, B., Bulfaro, G., Lardieri, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.219 (Depositor), 0.221 (DCC)
R-Value Work:
0.187 (Depositor), 0.194 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

OleP triple mutant F84Q/S240A/V291G in complex with LCA

Montemiglio, L.C., Costanzo, A., Fata, F., Freda, I., Demitri, N., Savino, C., Vallone, B., Bulfaro, G., Lardieri, A., Di Renzo, M., Barbizzi, L., Amadei, M.

To be published.

Macromolecule Content

Total Structure Weight: 279.89 kDa
Atom Count: 19,375
Modeled Residue Count: 2,382
Deposited Residue Count: 2,460
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P-450	A, B, C, D, E A, B, C, D, E, F	410	Streptomyces antibioticus	Mutation(s): 3 Gene Names: oleP
UniProt
Find proteins for Q59819 (Streptomyces antibioticus) Explore Q59819 Go to UniProtKB: Q59819
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q59819
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain VB [auth F] SDF format, chain PB [auth E] SDF format, chain PA [auth C] SDF format, chain G [auth A] SDF format, chain EB [auth D] SDF format, chain DA [auth B] MOL2 format, chain VB [auth F] MOL2 format, chain PB [auth E] MOL2 format, chain PA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain EB [auth D] MOL2 format, chain DA [auth B] mmCIF format, chain VB [auth F] mmCIF format, chain PB [auth E] mmCIF format, chain PA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain EB [auth D] mmCIF format, chain DA [auth B]	DA [auth B] EB [auth D] G [auth A] PA [auth C] PB [auth E] DA [auth B], EB [auth D], G [auth A], PA [auth C], PB [auth E], VB [auth F]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain DA [auth B] Focus chain EB [auth D] Focus chain G [auth A] Focus chain PA [auth C] Focus chain PB [auth E] Focus chain VB [auth F] Interactions & Density Focus chain DA [auth B] Focus chain EB [auth D] Focus chain G [auth A] Focus chain PA [auth C] Focus chain PB [auth E] Focus chain VB [auth F]
4OA Query on 4OA Download:Ideal Coordinates CCD File SDF format, chain WB [auth F] SDF format, chain QB [auth E] SDF format, chain QA [auth C] SDF format, chain H [auth A] SDF format, chain FB [auth D] SDF format, chain EA [auth B] MOL2 format, chain WB [auth F] MOL2 format, chain QB [auth E] MOL2 format, chain QA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain FB [auth D] MOL2 format, chain EA [auth B] mmCIF format, chain WB [auth F] mmCIF format, chain QB [auth E] mmCIF format, chain QA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain FB [auth D] mmCIF format, chain EA [auth B]	EA [auth B] FB [auth D] H [auth A] QA [auth C] QB [auth E] EA [auth B], FB [auth D], H [auth A], QA [auth C], QB [auth E], WB [auth F]	(3beta,5beta,14beta,17alpha)-3-hydroxycholan-24-oic acid C₂₄ H₄₀ O₃ SMEROWZSTRWXGI-HVATVPOCSA-N		Interactions Focus chain EA [auth B] Focus chain FB [auth D] Focus chain H [auth A] Focus chain QA [auth C] Focus chain QB [auth E] Focus chain WB [auth F] Interactions & Density Focus chain EA [auth B] Focus chain FB [auth D] Focus chain H [auth A] Focus chain QA [auth C] Focus chain QB [auth E] Focus chain WB [auth F]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain ZA [auth C] SDF format, chain Z [auth A] SDF format, chain YB [auth F] SDF format, chain YA [auth C] SDF format, chain Y [auth A] SDF format, chain XB [auth F] SDF format, chain XA [auth C] SDF format, chain X [auth A] SDF format, chain WA [auth C] SDF format, chain W [auth A] SDF format, chain VA [auth C] SDF format, chain V [auth A] SDF format, chain UB [auth E] SDF format, chain UA [auth C] SDF format, chain U [auth A] SDF format, chain TB [auth E] SDF format, chain TA [auth C] SDF format, chain T [auth A] SDF format, chain SB [auth E] SDF format, chain SA [auth C] SDF format, chain S [auth A] SDF format, chain RB [auth E] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain OB [auth D] SDF format, chain OA [auth B] SDF format, chain O [auth A] SDF format, chain NB [auth D] SDF format, chain NA [auth B] SDF format, chain N [auth A] SDF format, chain MB [auth D] SDF format, chain MA [auth B] SDF format, chain M [auth A] SDF format, chain LB [auth D] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain KB [auth D] SDF format, chain KA [auth B] SDF format, chain K [auth A] SDF format, chain JB [auth D] SDF format, chain JA [auth B] SDF format, chain J [auth A] SDF format, chain IB [auth D] SDF format, chain IA [auth B] SDF format, chain HB [auth D] SDF format, chain HA [auth B] SDF format, chain GA [auth B] SDF format, chain DB [auth C] SDF format, chain CB [auth C] SDF format, chain CA [auth A] SDF format, chain BB [auth C] SDF format, chain BA [auth A] SDF format, chain AB [auth C] SDF format, chain AA [auth A] MOL2 format, chain ZA [auth C] MOL2 format, chain Z [auth A] MOL2 format, chain YB [auth F] MOL2 format, chain YA [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain XB [auth F] MOL2 format, chain XA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain UB [auth E] MOL2 format, chain UA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain TB [auth E] MOL2 format, chain TA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain SB [auth E] MOL2 format, chain SA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain RB [auth E] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain OB [auth D] MOL2 format, chain OA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain NB [auth D] MOL2 format, chain NA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain MB [auth D] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LB [auth D] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain KB [auth D] MOL2 format, chain KA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain JB [auth D] MOL2 format, chain JA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain IB [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain CA [auth A] MOL2 format, chain BB [auth C] MOL2 format, chain BA [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain AA [auth A] mmCIF format, chain ZA [auth C] mmCIF format, chain Z [auth A] mmCIF format, chain YB [auth F] mmCIF format, chain YA [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain XB [auth F] mmCIF format, chain XA [auth C] mmCIF format, chain X [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain UB [auth E] mmCIF format, chain UA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain TB [auth E] mmCIF format, chain TA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain SB [auth E] mmCIF format, chain SA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain RB [auth E] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain OB [auth D] mmCIF format, chain OA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain NB [auth D] mmCIF format, chain NA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain MB [auth D] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LB [auth D] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain KB [auth D] mmCIF format, chain KA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain JB [auth D] mmCIF format, chain JA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain IB [auth D] mmCIF format, chain IA [auth B] mmCIF format, chain HB [auth D] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain DB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain CA [auth A] mmCIF format, chain BB [auth C] mmCIF format, chain BA [auth A] mmCIF format, chain AB [auth C] mmCIF format, chain AA [auth A]	AA [auth A] AB [auth C] BA [auth A] BB [auth C] CA [auth A] AA [auth A], AB [auth C], BA [auth A], BB [auth C], CA [auth A], CB [auth C], DB [auth C], GA [auth B], HA [auth B], HB [auth D], IA [auth B], IB [auth D], J [auth A], JA [auth B], JB [auth D], K [auth A], KA [auth B], KB [auth D], L [auth A], LA [auth B], LB [auth D], M [auth A], MA [auth B], MB [auth D], N [auth A], NA [auth B], NB [auth D], O [auth A], OA [auth B], OB [auth D], P [auth A], Q [auth A], R [auth A], RB [auth E], S [auth A], SA [auth C], SB [auth E], T [auth A], TA [auth C], TB [auth E], U [auth A], UA [auth C], UB [auth E], V [auth A], VA [auth C], W [auth A], WA [auth C], X [auth A], XA [auth C], XB [auth F], Y [auth A], YA [auth C], YB [auth F], Z [auth A], ZA [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RB [auth E] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth E] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TB [auth E] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UB [auth E] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain XB [auth F] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain YB [auth F] Focus chain Z [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RB [auth E] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth E] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TB [auth E] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UB [auth E] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain XB [auth F] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain YB [auth F] Focus chain Z [auth A] Focus chain ZA [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain RA [auth C] SDF format, chain I [auth A] SDF format, chain GB [auth D] SDF format, chain FA [auth B] MOL2 format, chain RA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain FA [auth B] mmCIF format, chain RA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain GB [auth D] mmCIF format, chain FA [auth B]	FA [auth B], GB [auth D], I [auth A], RA [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain GB [auth D] Focus chain I [auth A] Focus chain RA [auth C] Interactions & Density Focus chain FA [auth B] Focus chain GB [auth D] Focus chain I [auth A] Focus chain RA [auth C]