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- PDB-4qo7: Lactate Dehydrogenase A in complex with substituted 3-Hydroxy-2-m... -

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Basic information

Entry
Database: PDB / ID: 4qo7
TitleLactate Dehydrogenase A in complex with substituted 3-Hydroxy-2-mercaptocyclohex-2-enone compound 7
ComponentsL-lactate dehydrogenase A chain
Keywordsoxidoreductase/oxidoreductase inhibitor / oxidoreductase / Nicotinamide adenine dinucleotide / oxidoreductase-oxidoreductase inhibitor complex
Function / homology
Function and homology information


L-lactate dehydrogenase / oxidoreductase complex / Pyruvate metabolism / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / Regulation of pyruvate metabolism / glycolytic process / cadherin binding ...L-lactate dehydrogenase / oxidoreductase complex / Pyruvate metabolism / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / Regulation of pyruvate metabolism / glycolytic process / cadherin binding / mitochondrion / extracellular exosome / identical protein binding / membrane / nucleus / cytosol
Similarity search - Function
L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / 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 ...L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / 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
(2S)-2-HYDROXYPROPANOIC ACID / Chem-36V / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / L-lactate dehydrogenase A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsEigenbrot, C. / Ultsch, M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2014
Title: Identification of substituted 3-hydroxy-2-mercaptocyclohex-2-enones as potent inhibitors of human lactate dehydrogenase.
Authors: Dragovich, P.S. / Fauber, B.P. / Boggs, J. / Chen, J. / Corson, L.B. / Ding, C.Z. / Eigenbrot, C. / Ge, H. / Giannetti, A.M. / Hunsaker, T. / Labadie, S. / Li, C. / Liu, Y. / Liu, Y. / Ma, S. ...Authors: Dragovich, P.S. / Fauber, B.P. / Boggs, J. / Chen, J. / Corson, L.B. / Ding, C.Z. / Eigenbrot, C. / Ge, H. / Giannetti, A.M. / Hunsaker, T. / Labadie, S. / Li, C. / Liu, Y. / Liu, Y. / Ma, S. / Malek, S. / Peterson, D. / Pitts, K.E. / Purkey, H.E. / Robarge, K. / Salphati, L. / Sideris, S. / Ultsch, M. / VanderPorten, E. / Wang, J. / Wei, B. / Xu, Q. / Yen, I. / Yue, Q. / Zhang, H. / Zhang, X. / Zhou, A.
History
DepositionJun 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Sep 3, 2014Group: Database references
Revision 1.3Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
C: L-lactate dehydrogenase A chain
D: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,00116
Polymers146,4144
Non-polymers4,58712
Water12,556697
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26700 Å2
ΔGint-169 kcal/mol
Surface area44450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.481, 81.101, 120.307
Angle α, β, γ (deg.)90.00, 117.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#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: 36603.473 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDHA, PIG19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00338, L-lactate dehydrogenase

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Non-polymers , 6 types, 709 molecules

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


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-36V / trans-2-[(2-nitrophenyl)sulfanyl]-5-phenylcyclohexane-1,3-dione


Mass: 341.381 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H15NO4S
#5: Chemical ChemComp-2OP / (2S)-2-HYDROXYPROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / 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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG3350, sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 13, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. all: 78838 / Num. obs: 78834 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.074 / Net I/σ(I): 16

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M49

4m49


Resolution: 2.14→34.84 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.822 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.212 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 3964 5 %RANDOM
Rwork0.15789 ---
all0.161 78838 --
obs0.16038 74870 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.761 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å2-0 Å2-0.88 Å2
2--0.46 Å20 Å2
3----0.81 Å2
Refine analyzeLuzzati coordinate error free: 0.176 Å
Refinement stepCycle: LAST / Resolution: 2.14→34.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10262 0 304 697 11263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01910762
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210583
X-RAY DIFFRACTIONr_angle_refined_deg1.3622.00614596
X-RAY DIFFRACTIONr_angle_other_deg0.721324408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75351320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6825.123406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.993151951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5571543
X-RAY DIFFRACTIONr_chiral_restr0.1340.21699
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211816
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022212
LS refinement shellResolution: 2.142→2.257 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.27 561 -
Rwork0.197 10469 -
obs--95.83 %

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