8A8L

Crystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with a heme-coordinated fragment

PDB DOI: https://doi.org/10.2210/pdb8A8L/pdb

Classification: OXIDOREDUCTASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-06-23 Released: 2023-07-05
Deposition Author(s): Snee, M., Katariya, M., Levy, C.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.236 (Depositor), 0.230 (DCC)
R-Value Work:
0.198 (Depositor), 0.190 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with a heme-coordinated fragment

Snee, M., Katariya, M.

To be published.

Macromolecule Content

Total Structure Weight: 47.07 kDa
Atom Count: 3,616
Modelled Residue Count: 393
Deposited Residue Count: 400
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 P450 protein	A	400	Staphylococcus aureus	Mutation(s): 0 Gene Names: cypX_1, NCTC5664_01270, cypX EC: 1.14.15.13 (PDB Primary Data), 1.14 (UniProt)
UniProt
Find proteins for A0A380DQV1 (Staphylococcus aureus) Explore A0A380DQV1 Go to UniProtKB: A0A380DQV1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A380DQV1
Sequence Annotations Expand
Reference Sequence LOADING

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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
LBJ (Subject of Investigation/LOI) Query on LBJ Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	6-methoxy-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole C₁₂ H₁₄ N₂ O QYMDEOQLJUUNOF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain C [auth A]	C [auth A], E [auth A], F [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A]