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- PDB-1u5c: Plasmodium falciparum lactate dehydrogenase complexed with 3,7-di... -

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Basic information

Entry
Database: PDB / ID: 1u5c
TitlePlasmodium falciparum lactate dehydrogenase complexed with 3,7-dihydroxynaphthalene-2-carboxylic acid and NAD+
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
3,7-DIHYDROXY-2-NAPHTHOIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-lactate dehydrogenase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsConners, R. / Cameron, A. / Read, J. / 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. / Cameron, A. / Sessions, R.B. / Vivas, L. / Easton, A. / Croft, S.L. / Brady, R.L.
History
DepositionJul 27, 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)35,7143
Polymers34,8461
Non-polymers8682
Water2,378132
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)142,85612
Polymers139,3864
Non-polymers3,4708
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 area22170 Å2
ΔGint-123 kcal/mol
Surface area38440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.225, 86.017, 91.070
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 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: 34846.387 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-BIK / 3,7-DIHYDROXY-2-NAPHTHOIC ACID / 3,7-DIHYDROXYNAPHTHALENE-2-CARBOXYLIC ACID


Mass: 204.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.36 Å3/Da / Density % sol: 47.44 %
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: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Sep 14, 2001 / Details: Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 10105 / Num. obs: 9848 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rsym value: 0.127 / Net I/σ(I): 7.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 992 / Rsym value: 0.294 / % possible all: 99

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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: 2.65→29.36 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.872 / SU B: 11.843 / SU ML: 0.247 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23945 441 4.9 %RANDOM
Rwork0.15374 ---
all0.1579 9013 --
obs0.1579 8572 95.28 %-
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: 14.362 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å20 Å2
2--1.65 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.65→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 59 132 2496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222393
X-RAY DIFFRACTIONr_bond_other_d0.0020.022217
X-RAY DIFFRACTIONr_angle_refined_deg1.5872.0053244
X-RAY DIFFRACTIONr_angle_other_deg0.79335163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2015295
X-RAY DIFFRACTIONr_chiral_restr0.0750.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022567
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02414
X-RAY DIFFRACTIONr_nbd_refined0.3120.2591
X-RAY DIFFRACTIONr_nbd_other0.2370.22629
X-RAY DIFFRACTIONr_nbtor_other0.0870.21397
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2104
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.216
X-RAY DIFFRACTIONr_mcbond_it0.6531.51497
X-RAY DIFFRACTIONr_mcangle_it1.21722408
X-RAY DIFFRACTIONr_scbond_it1.7213896
X-RAY DIFFRACTIONr_scangle_it2.9414.5836
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.368 43
Rwork0.184 594
obs-637

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