5YQH | pdb_00005yqh

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

PDB DOI: https://doi.org/10.2210/pdb5YQH/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: 2.30 Å
R-Value Free:
0.237 (Depositor), 0.235 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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: 184.16 kDa
Atom Count: 13,011
Modeled Residue Count: 1,572
Deposited Residue Count: 1,640
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A, B, C, D	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain JA [auth D] SDF format, chain Q [auth B] SDF format, chain E [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain E [auth A] mmCIF format, chain BA [auth C] mmCIF format, chain JA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain E [auth A]	BA [auth C], E [auth A], JA [auth D], Q [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain BA [auth C] Focus chain E [auth A] Focus chain JA [auth D] Focus chain Q [auth B] Interactions & Density Focus chain BA [auth C] Focus chain E [auth A] Focus chain JA [auth D] Focus chain Q [auth B]
8ZX Query on 8ZX Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain KA [auth D] SDF format, chain H [auth A] MOL2 format, chain CA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain KA [auth D] MOL2 format, chain H [auth A] mmCIF format, chain CA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain KA [auth D] mmCIF format, chain H [auth A]	CA [auth C] F [auth A] G [auth A] H [auth A] KA [auth D] CA [auth C], F [auth A], G [auth A], H [auth A], KA [auth D], R [auth B], S [auth B], T [auth B]	4-methoxybenzamide C₈ H₉ N O₂ GUCPYIYFQVTFSI-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain KA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain CA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain KA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain M [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain M [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain M [auth A]	AA [auth B] GA [auth C] HA [auth C] IA [auth C] K [auth A] AA [auth B], GA [auth C], HA [auth C], IA [auth C], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], OA [auth D], P [auth A], X [auth B], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain J [auth A] SDF format, chain NA [auth D] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain MA [auth D] SDF format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain MA [auth D] MOL2 format, chain FA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain MA [auth D] mmCIF format, chain FA [auth C]	EA [auth C] FA [auth C] J [auth A] MA [auth D] NA [auth D] EA [auth C], FA [auth C], J [auth A], MA [auth D], NA [auth D], V [auth B], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain J [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain J [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain V [auth B] Focus chain W [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain I [auth A] SDF format, chain LA [auth D] SDF format, chain U [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain U [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain U [auth B]	DA [auth C], I [auth A], LA [auth D], U [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth C] Focus chain I [auth A] Focus chain LA [auth D] Focus chain U [auth B] Interactions & Density Focus chain DA [auth C] Focus chain I [auth A] Focus chain LA [auth D] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.237 (Depositor), 0.235 (DCC)
R-Value Work: 0.196 (Depositor), 0.200 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.928	α = 90
b = 143.242	β = 90
c = 171.889	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, Derived calculations, Refinement description