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- PDB-1t2d: Plasmodium falciparum lactate dehydrogenase complexed with NAD+ a... -

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Basic information

Entry
Database: PDB / ID: 1t2d
TitlePlasmodium falciparum lactate dehydrogenase complexed with NAD+ and oxalate
ComponentsL-lactate dehydrogenaseLactate dehydrogenase
KeywordsOXIDOREDUCTASE / Ternary complex
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase activity / carboxylic acid 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / OXALATE ION / L-lactate dehydrogenase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 21, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8214
Polymers34,9781
Non-polymers8443
Water5,314295
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)143,28416
Polymers139,9104
Non-polymers3,37412
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 area22590 Å2
ΔGint-114 kcal/mol
Surface area39120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.507, 86.583, 90.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
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 / 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-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9091 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9091 Å / Relative weight: 1
ReflectionResolution: 1.1→30 Å / Num. all: 127550 / Num. obs: 127177 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rsym value: 0.072 / Net I/σ(I): 22.5
Reflection shellResolution: 1.1→1.12 Å / Mean I/σ(I) obs: 2.1 / Num. unique all: 6036 / Rsym value: 0.473 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LDG

1ldg


Resolution: 1.1→29.49 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.31 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.028 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15169 6169 5 %RANDOM
Rwork0.14279 ---
all0.14324 122251 --
obs0.14324 116082 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 6.56 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.1→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 56 295 2734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222506
X-RAY DIFFRACTIONr_bond_other_d0.0020.022334
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9923397
X-RAY DIFFRACTIONr_angle_other_deg1.30535467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2385314
X-RAY DIFFRACTIONr_chiral_restr0.1050.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022709
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02431
X-RAY DIFFRACTIONr_nbd_refined0.2140.2529
X-RAY DIFFRACTIONr_nbd_other0.2380.22651
X-RAY DIFFRACTIONr_nbtor_other0.0840.21415
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0870.2196
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.231
X-RAY DIFFRACTIONr_mcbond_it0.5591.51560
X-RAY DIFFRACTIONr_mcangle_it0.98222529
X-RAY DIFFRACTIONr_scbond_it1.3843946
X-RAY DIFFRACTIONr_scangle_it2.2254.5868
X-RAY DIFFRACTIONr_rigid_bond_restr0.65522506
X-RAY DIFFRACTIONr_sphericity_free1.612295
X-RAY DIFFRACTIONr_sphericity_bonded1.04322465
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.228 407
Rwork0.222 7617
obs-8024

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