1SOW

T. gondii bradyzoite-specific LDH (LDH2) in complex with NAD and oxalate

PDB DOI: https://doi.org/10.2210/pdb1SOW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Toxoplasma gondii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-03-15 Released: 2005-03-15
Deposition Author(s): Kavanagh, K.L., Wilson, D.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.212
R-Value Work: 0.185
R-Value Observed: 0.185

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of apo and ternary forms of Toxoplasma gondii LDH2

Kavanagh, K.L., Wilson, D.K.

To be published.

Macromolecule Content

Total Structure Weight: 72.56 kDa
Atom Count: 5,329
Modelled Residue Count: 645
Deposited Residue Count: 656
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase	A, B	328	Toxoplasma gondii	Mutation(s): 0 EC: 1.1.1.27
UniProt
Find proteins for Q27797 (Toxoplasma gondii) Explore Q27797 Go to UniProtKB: Q27797
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% 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 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]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
OXL Query on OXL 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]	OXALATE ION C₂ O₄ MUBZPKHOEPUJKR-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.212
R-Value Work: 0.185
R-Value Observed: 0.185
Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.712	α = 90
b = 140.712	β = 90
c = 74.74	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
CNS	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-03-15

Deposition Author(s):

Kavanagh, K.L.

Wilson, D.K.

Revision History (Full details and data files)

Version 1.0: 2005-03-15
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

1SOW

T. gondii bradyzoite-specific LDH (LDH2) in complex with NAD and oxalate

Structure of apo and ternary forms of Toxoplasma gondii LDH2

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)