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- PDB-7epm: human LDHC complexed with NAD+ and ethylamino acetic acid -

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Basic information

Entry
Database: PDB / ID: 7epm
Titlehuman LDHC complexed with NAD+ and ethylamino acetic acid
ComponentsL-lactate dehydrogenase C chain
KeywordsOXIDOREDUCTASE / complex
Function / homology
Function and homology information


lactate biosynthetic process from pyruvate / lactate oxidation / flagellated sperm motility / ATP biosynthetic process / Pyruvate metabolism / L-lactate dehydrogenase / L-lactate dehydrogenase activity / motile cilium / carbohydrate metabolic process / extracellular exosome ...lactate biosynthetic process from pyruvate / lactate oxidation / flagellated sperm motility / ATP biosynthetic process / Pyruvate metabolism / L-lactate dehydrogenase / L-lactate dehydrogenase activity / motile cilium / carbohydrate metabolic process / extracellular exosome / nucleus / cytosol
Similarity search - Function
L-lactate dehydrogenase active site. / L-lactate dehydrogenase / 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
2-(ethylamino)-2-oxidanylidene-ethanoic acid / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-lactate dehydrogenase C chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsYu, Y. / Chen, Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Pharm Sin B / Year: 2022
Title: Identification of human LDHC4 as a potential target for anticancer drug discovery.
Authors: Tan, H. / Wang, H. / Ma, J. / Deng, H. / He, Q. / Chen, Q. / Zhang, Q.
History
DepositionApr 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,48215
Polymers75,0572
Non-polymers2,42613
Water48627
1
A: L-lactate dehydrogenase C chain
B: L-lactate dehydrogenase C chain
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)154,96530
Polymers150,1144
Non-polymers4,85126
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area29030 Å2
ΔGint-363 kcal/mol
Surface area42800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.891, 177.891, 179.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)

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Components

#1: Protein L-lactate dehydrogenase C chain / LDH-C / Cancer/testis antigen 32 / CT32 / LDH testis subunit / LDH-X


Mass: 37528.379 Da / Num. of mol.: 2 / Mutation: L55E, I331Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDHC, LDH3, LDHX / Production host: Escherichia coli (E. coli) / References: UniProt: P07864, L-lactate dehydrogenase
#2: Chemical ChemComp-J9X / 2-(ethylamino)-2-oxidanylidene-ethanoic acid


Mass: 117.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
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: 5.45 Å3/Da / Density % sol: 77.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M sodium chloride, 0.1 M HEPES pH 7.5, 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.998→50 Å / Num. obs: 34121 / % possible obs: 100 % / Redundancy: 21.3 % / Biso Wilson estimate: 60.94 Å2 / CC1/2: 0.987 / Net I/σ(I): 15
Reflection shellResolution: 2.998→3.07 Å / Num. unique obs: 2229 / CC1/2: 0.602

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I10

1i10


Resolution: 3→44.47 Å / SU ML: 0.3397 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.1232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2265 1358 4.04 %
Rwork0.2035 32279 -
obs0.2044 33637 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.6 Å2
Refinement stepCycle: LAST / Resolution: 3→44.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5076 0 149 27 5252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01055303
X-RAY DIFFRACTIONf_angle_d1.18787195
X-RAY DIFFRACTIONf_chiral_restr0.0764852
X-RAY DIFFRACTIONf_plane_restr0.0058877
X-RAY DIFFRACTIONf_dihedral_angle_d9.85283132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.110.35031270.31742996X-RAY DIFFRACTION93.92
3.11-3.230.30611470.29893175X-RAY DIFFRACTION99.43
3.23-3.380.29791250.26653225X-RAY DIFFRACTION100
3.38-3.550.24691180.24643241X-RAY DIFFRACTION99.91
3.55-3.780.2711310.21643230X-RAY DIFFRACTION99.82
3.78-4.070.22071490.19623222X-RAY DIFFRACTION99.88
4.07-4.480.19791170.1673270X-RAY DIFFRACTION99.88
4.48-5.120.18931490.16163272X-RAY DIFFRACTION99.8
5.12-6.450.21981440.19773317X-RAY DIFFRACTION99.63
6.45-44.470.18371510.16983331X-RAY DIFFRACTION95.08

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