7MYD | pdb_00007myd

Leishmania major dihydroorotate dehydrogenase in complex with 5-amino-2-(1H-pyrrol-1-yl)benzonitrile

PDB DOI: https://doi.org/10.2210/pdb7MYD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Leishmania major
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-05-20 Released: 2022-05-25
Deposition Author(s): Pinheiro, M.P., Cardoso, I.A., Hunter, W.N., Nonato, M.C.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.219 (Depositor), 0.220 (DCC)
R-Value Work:
0.178 (Depositor), 0.178 (DCC)

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

Leishmania major dihydroorotate dehydrogenase in complex with 5-amino-2-(1H-pyrrol-1-yl)benzonitrile

Pinheiro, M.P., Cardoso, I.A., Hunter, W.N., Nonato, M.C.

To be published.

Macromolecule Content

Total Structure Weight: 78.15 kDa
Atom Count: 5,135
Modeled Residue Count: 612
Deposited Residue Count: 708
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase (fumarate)	A [auth AAA], B [auth BBB]	354	Leishmania major	Mutation(s): 0 Gene Names: DHODH, LMJF_16_0530 EC: 1.3.98.1
UniProt
Find proteins for Q4QEW7 (Leishmania major) Explore Q4QEW7 Go to UniProtKB: Q4QEW7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4QEW7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain I [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain I [auth BBB] mmCIF format, chain C [auth AAA] mmCIF format, chain I [auth BBB]	C [auth AAA], I [auth BBB]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth AAA] Focus chain I [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain I [auth BBB]
SNQ (Subject of Investigation/LOI) Query on SNQ Download:Ideal Coordinates CCD File SDF format, chain H [auth AAA] MOL2 format, chain H [auth AAA] mmCIF format, chain H [auth AAA]	H [auth AAA]	5-azanyl-2-pyrrol-1-yl-benzenecarbonitrile C₁₁ H₉ N₃ VDMUMLCWGQEGDZ-UHFFFAOYSA-N		Interactions Focus chain H [auth AAA] Interactions & Density Focus chain H [auth AAA]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain E [auth AAA] SDF format, chain J [auth BBB] MOL2 format, chain D [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain J [auth BBB] mmCIF format, chain D [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain J [auth BBB]	D [auth AAA], E [auth AAA], J [auth BBB]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain J [auth BBB] Interactions & Density Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain J [auth BBB]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain K [auth BBB] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain K [auth BBB] mmCIF format, chain F [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain K [auth BBB]	F [auth AAA], G [auth AAA], K [auth BBB]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain K [auth BBB] Interactions & Density Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain K [auth BBB]