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- PDB-3om9: T. Gondii bradyzoite-specific LDH (LDH1) in complex with NAD and OXQ -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3om9
TitleT. Gondii bradyzoite-specific LDH (LDH1) in complex with NAD and OXQ
ComponentsLactate dehydrogenase
KeywordsOXIDOREDUCTASE / Glycolysis / NAD
Function / homology
Function and homology information


lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / nucleotide binding
Similarity search - Function
Malate dehydrogenase, type 3 / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain ...Malate dehydrogenase, type 3 / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 4-HYDROXY-1,2,5-OXADIAZOLE-3-CARBOXYLIC ACID / L-lactate dehydrogenase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsSusko, M.S. / Wilson, D.K.
CitationJournal: To be Published
Title: T.Gondii bradyzoite-specific LDH (LDH1) in complex with NAD and OXQ
Authors: Susko, M.S. / Wilson, D.K.
History
DepositionAug 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactate dehydrogenase
B: Lactate dehydrogenase
C: Lactate dehydrogenase
D: Lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,32712
Polymers142,1534
Non-polymers3,1748
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23810 Å2
ΔGint-100 kcal/mol
Surface area40890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.307, 124.458, 86.721
Angle α, β, γ (deg.)90.00, 105.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Lactate dehydrogenase


Mass: 35538.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: Lactate Dehydrogenase, TGGT1_115280 / Plasmid: PTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: P90613, L-lactate dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-OXQ / 4-HYDROXY-1,2,5-OXADIAZOLE-3-CARBOXYLIC ACID


Mass: 130.059 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2N2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.98→30 Å / Num. all: 95484 / Num. obs: 92707 / % possible obs: 98.45 %

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Processing

Software
NameClassification
HKL-2000data collection
X-PLORmodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→30 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2226 89885 Random
obs0.1961 92707 -
all-95484 -
Refinement stepCycle: LAST / Resolution: 1.98→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9882 0 212 427 10521

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