8JC3 | pdb_00008jc3

Crystal structure of the P450 BM3 heme domain mutant F87A-T268V in complex with Pyd-N-C4-Phe and hydroxylamine

PDB DOI: https://doi.org/10.2210/pdb8JC3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Priestia megaterium NBRC 15308 = ATCC 14581
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-05-10 Released: 2023-12-27
Deposition Author(s): Jiang, Y., Dong, S., Feng, Y., Cong, Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.212 (Depositor), 0.210 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (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

C(sp3)-H hydroxylation of Broad-Spectrum Alkanes Catalyzed by an Artificial P450 Peroxygenase Driven by omega-Pyridyl Fatty Acyl Amino Acids.

Qin, X., Jiang, Y., Chen, J., Yao, F., Jin, L., Cong, Z.

(2023) Mol Catal 550

DOI: https://doi.org/10.1016/j.mcat.2023.113618

Macromolecule Content

Total Structure Weight: 109.38 kDa
Atom Count: 8,281
Modelled Residue Count: 901
Deposited Residue Count: 930
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional cytochrome P450/NADPH--P450 reductase	A [auth B], B [auth A]	465	Priestia megaterium NBRC 15308 = ATCC 14581	Mutation(s): 2 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14779
Sequence Annotations Expand
Reference Sequence LOADING

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 C [auth B] SDF format, chain I [auth A] MOL2 format, chain C [auth B] MOL2 format, chain I [auth A] mmCIF format, chain C [auth B] mmCIF format, chain I [auth A]	C [auth B], I [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth B] Focus chain I [auth A] Interactions & Density Focus chain C [auth B] Focus chain I [auth A]
LXO (Subject of Investigation/LOI) Query on LXO Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain G [auth B] SDF format, chain K [auth A] SDF format, chain M [auth A] MOL2 format, chain E [auth B] MOL2 format, chain G [auth B] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] mmCIF format, chain E [auth B] mmCIF format, chain G [auth B] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A]	E [auth B], G [auth B], K [auth A], M [auth A]	4-(pyridin-4-ylamino)butanoic acid C₉ H₁₂ N₂ O₂ HPDCDJWQNLPXFS-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain G [auth B] Focus chain K [auth A] Focus chain M [auth A] Interactions & Density Focus chain E [auth B] Focus chain G [auth B] Focus chain K [auth A] Focus chain M [auth A]
PHE Query on PHE Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain N [auth A] SDF format, chain F [auth B] SDF format, chain L [auth A] MOL2 format, chain H [auth B] MOL2 format, chain N [auth A] MOL2 format, chain F [auth B] MOL2 format, chain L [auth A] mmCIF format, chain H [auth B] mmCIF format, chain N [auth A] mmCIF format, chain F [auth B] mmCIF format, chain L [auth A]	F [auth B], H [auth B], L [auth A], N [auth A]	PHENYLALANINE C₉ H₁₁ N O₂ COLNVLDHVKWLRT-QMMMGPOBSA-N		Interactions Focus chain F [auth B] Focus chain H [auth B] Focus chain L [auth A] Focus chain N [auth A] Interactions & Density Focus chain F [auth B] Focus chain H [auth B] Focus chain L [auth A] Focus chain N [auth A]
HOA (Subject of Investigation/LOI) Query on HOA Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain J [auth A] MOL2 format, chain D [auth B] MOL2 format, chain J [auth A] mmCIF format, chain D [auth B] mmCIF format, chain J [auth A]	D [auth B], J [auth A]	HYDROXYAMINE H₃ N O AVXURJPOCDRRFD-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain J [auth A] Interactions & Density Focus chain D [auth B] Focus chain J [auth A]