3C61 | pdb_00003c61

Crystal structure of dihydroorotate dehydrogenase from Leishmania donovani

PDB DOI: https://doi.org/10.2210/pdb3C61/pdb

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

Deposited: 2008-02-01 Released: 2008-02-26
Deposition Author(s): Arakaki, T.L., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.196 (Depositor), 0.199 (DCC)
R-Value Work:
0.166 (Depositor), 0.172 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Dihydroorotate dehydrogenase from Leishmania donovani.

Arakaki, T.L., Merritt, E.A., Ullman, B., Yates, P.A.

To be published.

Macromolecule Content

Total Structure Weight: 139.48 kDa
Atom Count: 10,785
Modeled Residue Count: 1,256
Deposited Residue Count: 1,256
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase	A, B, C, D	314	Leishmania donovani	Mutation(s): 0 EC: 1.3.99.11 (PDB Primary Data), 1.3.98.1 (UniProt)
UniProt
Find proteins for D0VWT2 (Leishmania donovani) Explore D0VWT2 Go to UniProtKB: D0VWT2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VWT2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain P [auth B] SDF format, chain I [auth A] SDF format, chain BA [auth D] MOL2 format, chain W [auth C] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain W [auth C] mmCIF format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain BA [auth D]	BA [auth D], I [auth A], P [auth B], W [auth C]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain BA [auth D] Focus chain I [auth A] Focus chain P [auth B] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain I [auth A] Focus chain P [auth B] Focus chain W [auth C]
ORO Query on ORO Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain X [auth C] SDF format, chain Q [auth B] SDF format, chain J [auth A] MOL2 format, chain CA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain J [auth A] mmCIF format, chain CA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain J [auth A]	CA [auth D], J [auth A], Q [auth B], X [auth C]	OROTIC ACID C₅ H₄ N₂ O₄ PXQPEWDEAKTCGB-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain J [auth A] Focus chain Q [auth B] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain J [auth A] Focus chain Q [auth B] Focus chain X [auth C]
DTU Query on DTU Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain K [auth A] MOL2 format, chain DA [auth D] MOL2 format, chain K [auth A] mmCIF format, chain DA [auth D] mmCIF format, chain K [auth A]	DA [auth D], K [auth A]	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-ZXZARUISSA-N		Interactions Focus chain DA [auth D] Focus chain K [auth A] Interactions & Density Focus chain DA [auth D] Focus chain K [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain R [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain R [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain R [auth B]	R [auth B], Y [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Focus chain Y [auth C] Interactions & Density Focus chain R [auth B] Focus chain Y [auth C]
AZI Query on AZI Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain V [auth C] SDF format, chain Z [auth D] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain E [auth A] SDF format, chain AA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain AA [auth D]	AA [auth D] E [auth A] F [auth A] G [auth A] L [auth B] AA [auth D], E [auth A], F [auth A], G [auth A], L [auth B], M [auth B], N [auth B], O [auth B], S [auth C], T [auth C], U [auth C], V [auth C], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.196 (Depositor), 0.199 (DCC)
R-Value Work: 0.166 (Depositor), 0.172 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.869	α = 90
b = 83.869	β = 90
c = 188.725	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-02-26

Deposition Author(s):

Arakaki, T.L.

Merritt, E.A.

Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History (Full details and data files)

Version 1.0: 2008-02-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description