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), 0.230 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.198 (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

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

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 E [auth A] SDF format, chain JA [auth D] SDF format, chain Q [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain Q [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain Q [auth B]	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 H [auth A] SDF format, chain KA [auth D] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	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 M [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] 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 M [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] 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 M [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]	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 FA [auth C] SDF format, chain J [auth A] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain EA [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), 0.230 (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

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Ligand Structure Quality Assessment

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