5YQA | pdb_00005yqa

The crystal structure of CYP199A4 binding with 4-n-Propyl benzoic acid

PDB DOI: https://doi.org/10.2210/pdb5YQA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhodopseudomonas palustris HaA2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-11-06 Released: 2019-02-27
Deposition Author(s): Zhou, W., Zhang, T., Qiao, R., Bell, S., Coleman, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free:
0.196 (Depositor), 0.201 (DCC)
R-Value Work:
0.178 (Depositor)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5YQA

Ligand Structure Quality Assessment

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

Literature

The crystal structure of CYP199A4 binding with 4-n-Propyl benzoic acid

Coleman, T., Zhang, T., Qiao, R., Zhou, W., Beii, S.

To be published.

Macromolecule Content

Total Structure Weight: 45.4 kDa
Atom Count: 3,570
Modeled Residue Count: 393
Deposited Residue Count: 410
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A	410	Rhodopseudomonas palustris HaA2	Mutation(s): 0 Gene Names: RPB_3613
UniProt
Find proteins for Q2IU02 (Rhodopseudomonas palustris (strain HaA2)) Explore Q2IU02 Go to UniProtKB: Q2IU02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2IU02
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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]
8ZU Query on 8ZU Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4-propylbenzoic acid C₁₀ H₁₂ O₂ ATZHGRNFEFVDDJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free: 0.196 (Depositor), 0.201 (DCC)
R-Value Work: 0.178 (Depositor)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.86	α = 90
b = 51.377	β = 92.07
c = 79.588	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-02-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-02-27
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.