8QRD

OleP in complex with testosterone in high salt crystallization conditions

PDB DOI: https://doi.org/10.2210/pdb8QRD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces antibioticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-10-06 Released: 2024-07-03
Deposition Author(s): Fata, F., Costanzo, A., Freda, I., Gugole, E., Bulfaro, G., Barbizzi, L., Di Renzo, M., Savino, C., Vallone, B., Montemiglio, L.C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.212
R-Value Work: 0.165
R-Value Observed: 0.168

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 in complex with testosterone in high salt crystallization conditions

Fata, F., Costanzo, A., Freda, I., Gugole, E., Bulfaro, G., Barbizzi, L., Di Renzo, M., Savino, C., Vallone, B., Montemiglio, L.C.

To be published.

Macromolecule Content

Total Structure Weight: 279.45 kDa
Atom Count: 20,262
Modelled Residue Count: 2,380
Deposited Residue Count: 2,460
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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): 0 Gene Names: oleP
UniProt
Find proteins for Q59819 (Streptomyces antibioticus) Explore Q59819 Go to UniProtKB: Q59819
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% 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 EB [auth E] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain KB [auth F] SDF format, chain P [auth B] SDF format, chain UA [auth D] MOL2 format, chain EB [auth E] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain KB [auth F] MOL2 format, chain P [auth B] MOL2 format, chain UA [auth D] mmCIF format, chain EB [auth E] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain KB [auth F] mmCIF format, chain P [auth B] mmCIF format, chain UA [auth D]	EB [auth E] FA [auth C] G [auth A] KB [auth F] P [auth B] EB [auth E], FA [auth C], G [auth A], KB [auth F], P [auth B], UA [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain EB [auth E] Focus chain FA [auth C] Focus chain G [auth A] Focus chain KB [auth F] Focus chain P [auth B] Focus chain UA [auth D] Interactions & Density Focus chain EB [auth E] Focus chain FA [auth C] Focus chain G [auth A] Focus chain KB [auth F] Focus chain P [auth B] Focus chain UA [auth D]
TES (Subject of Investigation/LOI) Query on TES Download Ideal Coordinates CCD File SDF format, chain FB [auth E] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain LB [auth F] SDF format, chain Q [auth B] SDF format, chain VA [auth D] MOL2 format, chain FB [auth E] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain LB [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain VA [auth D] mmCIF format, chain FB [auth E] mmCIF format, chain GA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain LB [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain VA [auth D]	FB [auth E] GA [auth C] H [auth A] LB [auth F] Q [auth B] FB [auth E], GA [auth C], H [auth A], LB [auth F], Q [auth B], VA [auth D]	TESTOSTERONE C₁₉ H₂₈ O₂ MUMGGOZAMZWBJJ-DYKIIFRCSA-N		Interactions Focus chain FB [auth E] Focus chain GA [auth C] Focus chain H [auth A] Focus chain LB [auth F] Focus chain Q [auth B] Focus chain VA [auth D] Interactions & Density Focus chain FB [auth E] Focus chain GA [auth C] Focus chain H [auth A] Focus chain LB [auth F] Focus chain Q [auth B] Focus chain VA [auth D]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth D] SDF format, chain BA [auth B] SDF format, chain BB [auth D] SDF format, chain CA [auth B] SDF format, chain CB [auth D] SDF format, chain DA [auth B] SDF format, chain GB [auth E] SDF format, chain HA [auth C] SDF format, chain HB [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain IB [auth E] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain MB [auth F] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain NB [auth F] SDF format, chain OA [auth C] SDF format, chain OB [auth F] SDF format, chain PA [auth C] SDF format, chain PB [auth F] SDF format, chain QA [auth C] SDF format, chain QB [auth F] SDF format, chain R [auth B] SDF format, chain RA [auth C] SDF format, chain S [auth B] SDF format, chain SA [auth C] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain GB [auth E] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain IB [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain MB [auth F] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain NB [auth F] MOL2 format, chain OA [auth C] MOL2 format, chain OB [auth F] MOL2 format, chain PA [auth C] MOL2 format, chain PB [auth F] MOL2 format, chain QA [auth C] MOL2 format, chain QB [auth F] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain GB [auth E] mmCIF format, chain HA [auth C] mmCIF format, chain HB [auth E] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain IB [auth E] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain MB [auth F] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain NB [auth F] mmCIF format, chain OA [auth C] mmCIF format, chain OB [auth F] mmCIF format, chain PA [auth C] mmCIF format, chain PB [auth F] mmCIF format, chain QA [auth C] mmCIF format, chain QB [auth F] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth C] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D]	AA [auth B] AB [auth D] BA [auth B] BB [auth D] CA [auth B] AA [auth B], AB [auth D], BA [auth B], BB [auth D], CA [auth B], CB [auth D], DA [auth B], GB [auth E], HA [auth C], HB [auth E], I [auth A], IA [auth C], IB [auth E], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], MB [auth F], N [auth A], NA [auth C], NB [auth F], OA [auth C], OB [auth F], PA [auth C], PB [auth F], QA [auth C], QB [auth F], R [auth B], RA [auth C], S [auth B], SA [auth C], T [auth B], U [auth B], V [auth B], W [auth B], WA [auth D], X [auth B], XA [auth D], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain GB [auth E] Focus chain HA [auth C] Focus chain HB [auth E] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain MB [auth F] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth F] Focus chain OA [auth C] Focus chain OB [auth F] Focus chain PA [auth C] Focus chain PB [auth F] Focus chain QA [auth C] Focus chain QB [auth F] Focus chain R [auth B] Focus chain RA [auth C] Focus chain S [auth B] Focus chain SA [auth C] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain GB [auth E] Focus chain HA [auth C] Focus chain HB [auth E] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain MB [auth F] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth F] Focus chain OA [auth C] Focus chain OB [auth F] Focus chain PA [auth C] Focus chain PB [auth F] Focus chain QA [auth C] Focus chain QB [auth F] Focus chain R [auth B] Focus chain RA [auth C] Focus chain S [auth B] Focus chain SA [auth C] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain DB [auth D] SDF format, chain EA [auth B] SDF format, chain JB [auth E] SDF format, chain O [auth A] SDF format, chain RB [auth F] SDF format, chain TA [auth C] MOL2 format, chain DB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain JB [auth E] MOL2 format, chain O [auth A] MOL2 format, chain RB [auth F] MOL2 format, chain TA [auth C] mmCIF format, chain DB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain JB [auth E] mmCIF format, chain O [auth A] mmCIF format, chain RB [auth F] mmCIF format, chain TA [auth C]	DB [auth D] EA [auth B] JB [auth E] O [auth A] RB [auth F] DB [auth D], EA [auth B], JB [auth E], O [auth A], RB [auth F], TA [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain DB [auth D] Focus chain EA [auth B] Focus chain JB [auth E] Focus chain O [auth A] Focus chain RB [auth F] Focus chain TA [auth C] Interactions & Density Focus chain DB [auth D] Focus chain EA [auth B] Focus chain JB [auth E] Focus chain O [auth A] Focus chain RB [auth F] Focus chain TA [auth C]