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- PDB-8fw6: Human Lactate Dehydrogenase A in Complex with Inhibitor CHK-336 -

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Basic information

Entry
Database: PDB / ID: 8fw6
TitleHuman Lactate Dehydrogenase A in Complex with Inhibitor CHK-336
ComponentsL-lactate dehydrogenase A chain
KeywordsOXIDOREDUCTASE / LDHA hLDHA Human Lactate dehydrogenase A
Function / homology
Function and homology information


L-lactate dehydrogenase / oxidoreductase complex / L-lactate dehydrogenase activity / Pyruvate metabolism / lactate metabolic process / pyruvate metabolic process / substantia nigra development / Regulation of pyruvate metabolism / glycolytic process / cadherin binding ...L-lactate dehydrogenase / oxidoreductase complex / L-lactate dehydrogenase activity / Pyruvate metabolism / lactate metabolic process / pyruvate metabolic process / substantia nigra development / Regulation of pyruvate metabolism / glycolytic process / cadherin binding / mitochondrion / extracellular exosome / identical protein binding / nucleus / membrane / cytosol
Similarity search - Function
L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / 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 domain superfamily
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Chem-YBO / L-lactate dehydrogenase A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsLowther, W.T. / Gumpena, R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Other private Canada
CitationJournal: To Be Published
Title: Human Lactate Dehydrogenase A in complex with inhibitor CHK-336
Authors: Lowther, W.T. / Gumpena, R.
History
DepositionJan 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-lactate dehydrogenase A chain
B: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,68024
Polymers75,1272
Non-polymers3,55322
Water5,837324
1
A: L-lactate dehydrogenase A chain
B: L-lactate dehydrogenase A chain
hetero molecules

A: L-lactate dehydrogenase A chain
B: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,36148
Polymers150,2544
Non-polymers7,10744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area20620 Å2
ΔGint-132 kcal/mol
Surface area45770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.174, 118.174, 94.788
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein L-lactate dehydrogenase A chain / LDH-A / Cell proliferation-inducing gene 19 protein / LDH muscle subunit / LDH-M / Renal carcinoma ...LDH-A / Cell proliferation-inducing gene 19 protein / LDH muscle subunit / LDH-M / Renal carcinoma antigen NY-REN-59


Mass: 37563.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDHA, PIG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00338, L-lactate dehydrogenase

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Non-polymers , 5 types, 346 molecules

#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-YBO / (2P)-2-{5-(cyclopropylmethyl)-3-(4-fluorophenyl)-4-[(3-fluoro-4-sulfamoylphenyl)methyl]-1H-pyrazol-1-yl}-1,3-thiazole-4-carboxylic acid


Mass: 530.567 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C24H20F2N4O4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4.6 / Details: 0.1 M Sodium Acetate pH 4.6 30% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 4, 2019
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 32736 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 29.35 Å2 / Rmerge(I) obs: 0.175 / Rrim(I) all: 0.181 / Net I/σ(I): 14
Reflection shellResolution: 2.34→2.38 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 2.29 / Num. unique obs: 1629 / CC1/2: 0.76 / CC star: 0.929 / Rrim(I) all: 0.805 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→45.07 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.943 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20598 1562 4.8 %RANDOM
Rwork0.15356 ---
obs0.15601 30951 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.609 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.34→45.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5122 0 235 324 5681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125458
X-RAY DIFFRACTIONr_bond_other_d0.0120.0165206
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.6797380
X-RAY DIFFRACTIONr_angle_other_deg0.4651.5812119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9275664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.6421022
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03410970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025915
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02969
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7063.3422653
X-RAY DIFFRACTIONr_mcbond_other2.7053.3422653
X-RAY DIFFRACTIONr_mcangle_it3.9184.9963315
X-RAY DIFFRACTIONr_mcangle_other3.9184.9993316
X-RAY DIFFRACTIONr_scbond_it3.5833.8212805
X-RAY DIFFRACTIONr_scbond_other3.5823.8212806
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3895.524059
X-RAY DIFFRACTIONr_long_range_B_refined7.04650.2386090
X-RAY DIFFRACTIONr_long_range_B_other7.04850.2276087
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.34→2.399 Å
RfactorNum. reflection% reflection
Rfree0.254 130 -
Rwork0.212 2243 -
obs--98.75 %

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