3GZ3 | pdb_00003gz3

Leishmania major Dihydroorotate Dehydrogenase in complex with orotate

• PDB DOI: https://doi.org/10.2210/pdb3GZ3/pdb

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


• Deposited: 2009-04-06 Released: 2010-04-28 
• Deposition Author(s): Cordeiro, A.T., Feliciano, P.R., Nonato, M.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.204 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Leismania major dihydroorotate in complex with orotate

Cordeiro, A.T., Feliciano, P.R., Nonato, M.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.91 kDa 
• Atom Count: 5,128 
• Modeled Residue Count: 598 
• Deposited Residue Count: 708 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase, putative	A, B	354	Leishmania major	Mutation(s): 0  Gene Names: LmjF16.0530, pyrD EC: 1.3.3.1 (PDB Primary Data), 1.3.98.1 (UniProt)
UniProt
Find proteins for Q4QEW7 (Leishmania major) Explore Q4QEW7  Go to UniProtKB:  Q4QEW7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], G [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
ORO	D [auth A], H [auth B]	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N
GOL	E [auth A], F [auth A], I [auth B], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.204 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.167	α = 90
b = 142.167	β = 90
c = 69.157	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-28 
Deposition Author(s): Cordeiro, A.T., Feliciano, P.R., Nonato, M.C.

Revision History  

• Version 1.0: 2010-04-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description