3CZM | pdb_00003czm

T. Gondii bradyzoite-specific LDH (LDH2) in complex with NAD and OXQ

PDB DOI: https://doi.org/10.2210/pdb3CZM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Toxoplasma gondii
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-04-29 Released: 2009-06-02
Deposition Author(s): Wilson, D.K., Susko, M.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.223 (Depositor), 0.161 (DCC)
R-Value Work:
0.166 (Depositor)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

T. Gondii bradyzoite-specific LDH (LDH2) in complex with NAD and OXQ

Wilson, D.K., Susko, M.S.

To be published.

Macromolecule Content

Total Structure Weight: 72.34 kDa
Atom Count: 5,283
Modeled Residue Count: 645
Deposited Residue Count: 652
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase	A, B	326	Toxoplasma gondii	Mutation(s): 1 Gene Names: Lactate Dehydrogenase EC: 1.1.1.27
UniProt
Find proteins for Q27797 (Toxoplasma gondii) Explore Q27797 Go to UniProtKB: Q27797
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q27797
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
OXQ Query on OXQ Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	4-HYDROXY-1,2,5-OXADIAZOLE-3-CARBOXYLIC ACID C₃ H₂ N₂ O₄ IBRWUZLLHSXPKL-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.223 (Depositor), 0.161 (DCC)
R-Value Work: 0.166 (Depositor)
R-Value Observed: 0.169 (Depositor)

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.949	α = 90
b = 140.949	β = 90
c = 75.01	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
EPMR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-06-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-06-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations
Version 1.3: 2023-08-30
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.