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- PDB-1xiv: Plasmodium falciparum lactate dehydrogenase complexed with 2-({4-... -

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Basic information

Entry
Database: PDB / ID: 1xiv
TitlePlasmodium falciparum lactate dehydrogenase complexed with 2-({4-chloro-[hydroxy(methoxy)methyl]cyclohexyl}amino)ethane-1,1,2-triol
ComponentsL-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / Protein-ligand complex
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / lactate 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
Chem-RB2 / L-lactate dehydrogenase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsConners, R. / Cameron, A. / Read, J.A. / Schambach, F. / Sessions, R.B. / Brady, R.L.
CitationJournal: MOL.BIOCHEM.PARASITOL. / Year: 2005
Title: Mapping the binding site for gossypol-like inhibitors of Plasmodium falciparum lactate dehydrogenase
Authors: Conners, R. / Schambach, F. / Read, J.A. / Cameron, A. / Sessions, R.B. / Vivas, L. / Easton, A. / Croft, S.L. / Brady, R.L.
History
DepositionSep 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: 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)35,4173
Polymers35,0561
Non-polymers3622
Water6,485360
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)141,67012
Polymers140,2224
Non-polymers1,4478
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 area18720 Å2
ΔGint-124 kcal/mol
Surface area40060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.568, 85.393, 92.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-778-

HOH

DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the following operations and lattice translations: x,-y,-z/1,0,0 -x,y,-z/0,1,0 -x,-y,z/1,1,0

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Components

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


Mass: 35055.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: pKK223 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q27743, L-lactate dehydrogenase
#2: Chemical ChemComp-RB2 / 2-({4-CHLORO-2-[HYDROXY(METHOXY)METHYL]CYCLOHEXYL}AMINO)ETHANE-1,1,2-TRIOL


Mass: 269.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20ClNO5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.41 Å3/Da / Density % sol: 48.6 %
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: MARRESEARCH / Detector: IMAGE PLATE / Date: May 21, 2001
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 35317 / Num. obs: 33657 / % possible obs: 95.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rsym value: 0.058 / Net I/σ(I): 23.2
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 4018 / Rsym value: 0.207 / % possible all: 92.2

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Processing

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

1ldg


Resolution: 1.7→29.36 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.639 / SU ML: 0.055 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.092 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17884 1680 5.1 %RANDOM
Rwork0.14387 ---
all0.14561 33009 --
obs0.14561 31329 93.46 %-
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: 13.233 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--0.59 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 23 360 2703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222350
X-RAY DIFFRACTIONr_bond_other_d0.0020.022211
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.9783172
X-RAY DIFFRACTIONr_angle_other_deg1.24235150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5225297
X-RAY DIFFRACTIONr_chiral_restr0.0840.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022546
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02403
X-RAY DIFFRACTIONr_nbd_refined0.330.2534
X-RAY DIFFRACTIONr_nbd_other0.2380.22477
X-RAY DIFFRACTIONr_nbtor_other0.0860.21325
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2231
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.232
X-RAY DIFFRACTIONr_mcbond_it0.7521.51506
X-RAY DIFFRACTIONr_mcangle_it1.35722422
X-RAY DIFFRACTIONr_scbond_it2.3823844
X-RAY DIFFRACTIONr_scangle_it3.8774.5750
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.231 136
Rwork0.174 2089
obs-2089

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