8Q2F | pdb_00008q2f

Cytochrome P450 BM3 aMOx-A heme domain

PDB DOI: https://doi.org/10.2210/pdb8Q2F/pdb

Classification: OXIDOREDUCTASE
Organism(s): Priestia megaterium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-08-02 Released: 2025-01-15
Deposition Author(s): Klaus, C., Kowal, J.L., Hammer, S.C., Niemann, H.H.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.43 Å
R-Value Free:
0.226 (Depositor), 0.228 (DCC)
R-Value Work:
0.175 (Depositor), 0.177 (DCC)
R-Value Observed:
0.177 (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

Directed Evolution Enables Dynamic Control of Transient Intermediates for Anti-Markovnikov Wacker-Tsuji-Type Oxidation of Unactivated Alkenes

Klaus, C., Soler, J., Kubik, G., Gumulya, Y., Hui, Y., Watkins-Dulaney, E.J., Heitland, ML., Sommer, M., Klein, A., Kowal, J.L., Niemann, H.H., Arnold, F.H., Garcia-Borras.M., Hammer, S.C.

(2024) ChemRxiv

DOI: https://doi.org/10.26434/chemrxiv-2024-j0229-v2

Macromolecule Content

Total Structure Weight: 332.59 kDa
Atom Count: 22,710
Modeled Residue Count: 2,757
Deposited Residue Count: 2,832
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional cytochrome P450/NADPH--P450 reductase	A, B, C, D, E A, B, C, D, E, F	472	Priestia megaterium	Mutation(s): 26 Gene Names: cyp102A1, cyp102, BG04_163 EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (PDB Primary Data)
UniProt
Find proteins for P14779 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19)) Explore P14779 Go to UniProtKB: P14779
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14779
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain G [auth A] SDF format, chain LA [auth E] SDF format, chain P [auth B] SDF format, chain VA [auth F] SDF format, chain Y [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain Y [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain Y [auth C]	DA [auth D] G [auth A] LA [auth E] P [auth B] VA [auth F] DA [auth D], G [auth A], LA [auth E], P [auth B], VA [auth F], Y [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain DA [auth D] Focus chain G [auth A] Focus chain LA [auth E] Focus chain P [auth B] Focus chain VA [auth F] Focus chain Y [auth C] Interactions & Density Focus chain DA [auth D] Focus chain G [auth A] Focus chain LA [auth E] Focus chain P [auth B] Focus chain VA [auth F] Focus chain Y [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth F] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain TA [auth E] SDF format, chain UA [auth E] SDF format, chain X [auth B] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain TA [auth E] MOL2 format, chain UA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain AB [auth F] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain TA [auth E] mmCIF format, chain UA [auth E] mmCIF format, chain X [auth B] mmCIF format, chain Z [auth C]	AA [auth C] AB [auth F] BA [auth C] CA [auth C] IA [auth D] AA [auth C], AB [auth F], BA [auth C], CA [auth C], IA [auth D], JA [auth D], KA [auth D], M [auth A], N [auth A], O [auth A], TA [auth E], UA [auth E], X [auth B], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain X [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain X [auth B] Focus chain Z [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain MA [auth E] SDF format, chain NA [auth E] SDF format, chain PA [auth E] SDF format, chain Q [auth B] SDF format, chain QA [auth E] SDF format, chain R [auth B] SDF format, chain RA [auth E] SDF format, chain S [auth B] SDF format, chain WA [auth F] MOL2 format, chain EA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain WA [auth F] mmCIF format, chain EA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain NA [auth E] mmCIF format, chain PA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain WA [auth F]	EA [auth D] H [auth A] I [auth A] L [auth A] MA [auth E] EA [auth D], H [auth A], I [auth A], L [auth A], MA [auth E], NA [auth E], PA [auth E], Q [auth B], QA [auth E], R [auth B], RA [auth E], S [auth B], WA [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth A] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain WA [auth F] Interactions & Density Focus chain EA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth A] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain WA [auth F]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain OA [auth E] SDF format, chain SA [auth E] 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 XA [auth F] SDF format, chain YA [auth F] SDF format, chain ZA [auth F] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain SA [auth E] 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 XA [auth F] MOL2 format, chain YA [auth F] MOL2 format, chain ZA [auth F] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain SA [auth E] 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 XA [auth F] mmCIF format, chain YA [auth F] mmCIF format, chain ZA [auth F]	FA [auth D] GA [auth D] HA [auth D] J [auth A] K [auth A] FA [auth D], GA [auth D], HA [auth D], J [auth A], K [auth A], OA [auth E], SA [auth E], T [auth B], U [auth B], V [auth B], W [auth B], XA [auth F], YA [auth F], ZA [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain OA [auth E] Focus chain SA [auth E] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain XA [auth F] Focus chain YA [auth F] Focus chain ZA [auth F] Interactions & Density Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain OA [auth E] Focus chain SA [auth E] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain XA [auth F] Focus chain YA [auth F] Focus chain ZA [auth F]