7S87

Crystal Structure of Dihydroorotate dehydrogenase from Plasmodium falciparum in complex with Orotate, FMN, and inhibitor NCGC00600348-01

PDB DOI: https://doi.org/10.2210/pdb7S87/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2021-09-17 Released: 2021-09-29
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.230
R-Value Work: 0.170
R-Value Observed: 0.173

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 Dihydroorotate dehydrogenase from Plasmodium falciparum in complex with Orotate, FMN, and inhibitor NCGC00600348-01

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Shek, R., Abendroth, J., Lorimer, D., Edwards, T.E., Eastman, R., Van Voorhis, W.

To be published.

Macromolecule Content

Total Structure Weight: 94.25 kDa
Atom Count: 5,964
Modelled Residue Count: 752
Deposited Residue Count: 802
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase (quinone), mitochondrial	A, B	401	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: PFF0160c EC: 1.3.5.2 Membrane Entity: Yes
UniProt
Find proteins for Q08210 (Plasmodium falciparum (isolate 3D7)) Explore Q08210 Go to UniProtKB: Q08210
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08210
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P4K Query on P4K 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]	polyethylene glycol C₃₀ H₆₂ O₁₅ WWPGFZAAWXFBTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain L [auth B]	D [auth A], L [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain D [auth A] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain L [auth B]
8IE (Subject of Investigation/LOI) Query on 8IE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A], I [auth A], J [auth B], K [auth B]	(4R)-3-methyl-5-[(4R)-4-methyl-3,4-dihydroisoquinolin-2(1H)-yl]thieno[2,3-e][1,2,4]triazolo[4,3-c]pyrimidine C₁₈ H₁₇ N₅ S GGQQENQZNLSCPW-NSHDSACASA-N		Interactions Focus chain C [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B]
ORO Query on ORO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B]	E [auth A], M [auth B]	OROTIC ACID C₅ H₄ N₂ O₄ PXQPEWDEAKTCGB-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain M [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B]	H [auth A], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain N [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]