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- PDB-8zkj: The crystal structure of apo-LDHC -

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Basic information

Entry
Database: PDB / ID: 8zkj
TitleThe crystal structure of apo-LDHC
ComponentsL-lactate dehydrogenase C chain
KeywordsSTRUCTURAL PROTEIN / LDHC
Function / homology
Function and homology information


lactate biosynthetic process from pyruvate / pyruvate catabolic process / L-lactate dehydrogenase / ATP biosynthetic process / oxidoreductase complex / flagellated sperm motility / L-lactate dehydrogenase (NAD+) activity / pyruvate metabolic process / Pyruvate metabolism / lactate metabolic process ...lactate biosynthetic process from pyruvate / pyruvate catabolic process / L-lactate dehydrogenase / ATP biosynthetic process / oxidoreductase complex / flagellated sperm motility / L-lactate dehydrogenase (NAD+) activity / pyruvate metabolic process / Pyruvate metabolism / lactate metabolic process / motile cilium / mitochondrion / extracellular exosome / nucleus / 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
L-lactate dehydrogenase C chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsWu, C.Y. / Wang, H.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of human LDHC at 2.38 Angstroms resolution
Authors: Wu, C.Y. / Wang, H.L.
History
DepositionMay 16, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: 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 C chain
B: L-lactate dehydrogenase C chain


Theoretical massNumber of molelcules
Total (without water)75,0572
Polymers75,0572
Non-polymers00
Water34219
1
A: L-lactate dehydrogenase C chain
B: L-lactate dehydrogenase C chain

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


Theoretical massNumber of molelcules
Total (without water)150,1144
Polymers150,1144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area18940 Å2
ΔGint-120 kcal/mol
Surface area48600 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-49 kcal/mol
Surface area28130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.000, 86.000, 194.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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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
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
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: 0.97954 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 2.38→58.05 Å / Num. obs: 770756 / % possible obs: 100 % / Redundancy: 25.5 % / CC1/2: 0.997 / Net I/σ(I): 11.3
Reflection shellResolution: 2.38→2.44 Å / Num. unique obs: 2181 / CC1/2: 0.721

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EPM

7epm


Resolution: 2.38→58.05 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2613 1999 6.62 %
Rwork0.2082 --
obs0.2117 30180 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.38→58.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5054 0 0 19 5073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d14.6441892
X-RAY DIFFRACTIONf_chiral_restr0.054832
X-RAY DIFFRACTIONf_plane_restr0.006865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.440.33241400.28191964X-RAY DIFFRACTION100
2.44-2.510.28931380.25871952X-RAY DIFFRACTION100
2.51-2.580.31241410.25481991X-RAY DIFFRACTION100
2.58-2.660.3061400.24911965X-RAY DIFFRACTION100
2.66-2.760.31011410.26831979X-RAY DIFFRACTION100
2.76-2.870.34431400.26671993X-RAY DIFFRACTION100
2.87-30.35861410.26051979X-RAY DIFFRACTION100
3-3.160.33481410.24761988X-RAY DIFFRACTION100
3.16-3.350.30481410.2421994X-RAY DIFFRACTION100
3.35-3.610.28621440.22742025X-RAY DIFFRACTION100
3.61-3.980.2481430.20172014X-RAY DIFFRACTION100
3.98-4.550.21251460.17762048X-RAY DIFFRACTION100
4.55-5.730.21761470.17272082X-RAY DIFFRACTION100

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