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- PDB-1t26: Plasmodium falciparum lactate dehydrogenase complexed with NADH a... -

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Basic information

Entry
Database: PDB / ID: 1t26
TitlePlasmodium falciparum lactate dehydrogenase complexed with NADH and 4-hydroxy-1,2,5-thiadiazole-3-carboxylic acid
ComponentsL-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / protein-ligand complex
Function / homology
Function and homology information


L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process
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
4-HYDROXY-1,2,5-THIADIAZOLE-3-CARBOXYLIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / L-lactate dehydrogenase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCameron, A. / Read, J. / Tranter, R. / Winter, V.J. / Sessions, R.B. / Brady, R.L. / Vivas, L. / Easton, A. / Kendrick, H. / Croft, S.L. ...Cameron, A. / Read, J. / Tranter, R. / Winter, V.J. / Sessions, R.B. / Brady, R.L. / Vivas, L. / Easton, A. / Kendrick, H. / Croft, S.L. / Barros, D. / Lavandera, J.L. / Martin, J.J. / Risco, F. / Garcia-Ochoa, S. / Gamo, F.J. / Sanz, L. / Leon, L. / Ruiz, J.R. / Gabarro, R. / Mallo, A. / De Las Heras, F.G.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Identification and Activity of a Series of Azole-based Compounds with Lactate Dehydrogenase-directed Anti-malarial Activity.
Authors: Cameron, A. / Read, J. / Tranter, R. / Winter, V.J. / Sessions, R.B. / Brady, R.L. / Vivas, L. / Easton, A. / Kendrick, H. / Croft, S.L. / Barros, D. / Lavandera, J.L. / Martin, J.J. / ...Authors: Cameron, A. / Read, J. / Tranter, R. / Winter, V.J. / Sessions, R.B. / Brady, R.L. / Vivas, L. / Easton, A. / Kendrick, H. / Croft, S.L. / Barros, D. / Lavandera, J.L. / Martin, J.J. / Risco, F. / Garcia-Ochoa, S. / Gamo, F.J. / Sanz, L. / Leon, L. / Ruiz, J.R. / Gabarro, R. / Mallo, A. / De Las Heras, F.G.
History
DepositionApr 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7893
Polymers34,9781
Non-polymers8122
Water4,864270
1
A: L-lactate dehydrogenase
hetero molecules

A: L-lactate dehydrogenase
hetero molecules

A: L-lactate dehydrogenase
hetero molecules

A: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,15712
Polymers139,9104
Non-polymers3,2468
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area20890 Å2
ΔGint-140 kcal/mol
Surface area39540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.625, 86.631, 91.584
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-670-

HOH

DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations

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Components

#1: Protein L-lactate dehydrogenase / LDH-P


Mass: 34977.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: LDH / Plasmid: pKK223 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q27743, L-lactate dehydrogenase
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-GBD / 4-HYDROXY-1,2,5-THIADIAZOLE-3-CARBOXYLIC ACID


Mass: 146.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2N2O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.2 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MPD, Hepes, Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.8→29.488 Å / Num. all: 29800 / Num. obs: 27772 / % possible obs: 97.32 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rsym value: 0.064 / Net I/σ(I): 28.3
Reflection shellResolution: 1.8→1.89 Å / Mean I/σ(I) obs: 9.2 / Rsym value: 0.141 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LDQ

1ldq


Resolution: 1.8→29.488 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2095 1388 RANDOM
Rwork0.1744 --
obs-27772 -
Refinement stepCycle: LAST / Resolution: 1.8→29.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 53 270 2711

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