6EBS | pdb_00006ebs

Crystal structure of Leishmania major dihydroorotate dehydrogenase mutant H174A in complex with orotate

PDB DOI: https://doi.org/10.2210/pdb6EBS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Leishmania major
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-08-07 Released: 2019-08-21
Deposition Author(s): Reis, R.A.G., Pinheiro, M.P., de Souza, A.L., Hunter, W.N., Nonato, M.C.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.205 (Depositor)
R-Value Work:
0.166 (Depositor)
R-Value Observed:
0.168 (Depositor)

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

Crystal structure of Leishmania major dihydroorotate dehydrogenase mutant H174A in complex with orotate

Reis, R.A.G., Pinheiro, M.P., de Souza, A.L., Hunter, W.N., Nonato, M.C.

To be published.

Macromolecule Content

Total Structure Weight: 78.41 kDa
Atom Count: 5,469
Modeled Residue Count: 626
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, B	354	Leishmania major	Mutation(s): 1 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 5 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 A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain K [auth B]	C [auth A], K [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
ORO Query on ORO 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]	OROTIC ACID C₅ H₄ N₂ O₄ PXQPEWDEAKTCGB-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain L [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	H [auth A] I [auth A] J [auth A] N [auth B] O [auth B] H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B]	E [auth A], F [auth A], G [auth A], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.205 (Depositor)
R-Value Work: 0.166 (Depositor)
R-Value Observed: 0.168 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.279	α = 90
b = 144.279	β = 90
c = 69.913	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-08-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	11/23504-9
Sao Paulo Research Foundation (FAPESP)	Brazil	07/08703-0

Revision History (Full details and data files)

Version 1.0: 2019-08-21
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description