6L0J

Crystal structure of Dihydroorotase in complex with malate at pH7.5 from Saccharomyces cerevisiae

PDB DOI: https://doi.org/10.2210/pdb6L0J/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-09-26 Released: 2020-12-02
Deposition Author(s): Guan, H.H., Huang, Y.H., Huang, C.Y., Chen, C.J.
Funding Organization(s): Ministry of Science and Technology (Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.229
R-Value Work: 0.183
R-Value Observed: 0.185

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural Analysis of Saccharomyces cerevisiae Dihydroorotase Reveals Molecular Insights into the Tetramerization Mechanism

Guan, H.H., Huang, Y.H., Lin, E.S., Chen, C.J., Huang, C.Y.

(2021) Molecules

DOI: https://doi.org/10.3390/molecules26237249

Macromolecule Content

Total Structure Weight: 166.97 kDa
Atom Count: 12,616
Modelled Residue Count: 1,454
Deposited Residue Count: 1,488
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotase	A, B [auth D], C [auth B], D [auth C]	372	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: URA4, YLR420W, L9931.1 EC: 3.5.2.3
UniProt
Find proteins for P20051 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20051 Go to UniProtKB: P20051
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20051
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMR (Subject of Investigation/LOI) Query on LMR Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth D] SDF format, chain M [auth B] SDF format, chain P [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth D] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth D] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C]	G [auth A], J [auth D], M [auth B], P [auth C]	(2S)-2-hydroxybutanedioic acid C₄ H₆ O₅ BJEPYKJPYRNKOW-REOHCLBHSA-N		Interactions Focus chain G [auth A] Focus chain J [auth D] Focus chain M [auth B] Focus chain P [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth D] Focus chain M [auth B] Focus chain P [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth D] SDF format, chain I [auth D] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth D] MOL2 format, chain I [auth D] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth D] mmCIF format, chain I [auth D] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C]	E [auth A] F [auth A] H [auth D] I [auth D] K [auth B] E [auth A], F [auth A], H [auth D], I [auth D], K [auth B], L [auth B], N [auth C], O [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth D] Focus chain I [auth D] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth D] Focus chain I [auth D] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C]