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- PDB-9qyk: Crystal structure of human L-lactate Dehydrogenase B protein in c... -

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Basic information

Entry
Database: PDB / ID: 9qyk
TitleCrystal structure of human L-lactate Dehydrogenase B protein in complex with NADH, oxamate and sertraline
ComponentsL-lactate dehydrogenase B chain
KeywordsOXIDOREDUCTASE / Sertraline / modulator / complex
Function / homology
Function and homology information


pyruvate catabolic process / oxidoreductase complex / L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / Pyruvate metabolism / lactate metabolic process / NAD+ metabolic process / NAD binding / kinase binding / mitochondrial inner membrane ...pyruvate catabolic process / oxidoreductase complex / L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / Pyruvate metabolism / lactate metabolic process / NAD+ metabolic process / NAD binding / kinase binding / mitochondrial inner membrane / membrane raft / mitochondrion / extracellular exosome / membrane / identical protein binding / cytoplasm / 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 / OXAMIC ACID / Chem-SRE / L-lactate dehydrogenase B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsVan Gysel, M. / Wouters, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of human L-lactate Dehydrogenase B protein in complex with NADH, oxamate and sertraline
Authors: Van Gysel, M. / Wouters, J.
History
DepositionApr 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2026Provider: 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 B chain
B: L-lactate dehydrogenase B chain
C: L-lactate dehydrogenase B chain
D: L-lactate dehydrogenase B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,06713
Polymers153,8854
Non-polymers3,1829
Water15,637868
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24690 Å2
ΔGint-138 kcal/mol
Surface area47560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.760, 119.350, 159.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
L-lactate dehydrogenase B chain / LDH-B / LDH heart subunit / LDH-H / Renal carcinoma antigen NY-REN-46


Mass: 38471.246 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDHB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07195, L-lactate dehydrogenase
#2: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3NO3
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical ChemComp-SRE / (1S,4S)-4-(3,4-dichlorophenyl)-N-methyl-1,2,3,4-tetrahydronaphthalen-1-amine / Sertraline


Mass: 306.230 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H17Cl2N / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 868 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium formate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.06→48.79 Å / Num. obs: 100190 / % possible obs: 99.75 % / Redundancy: 13.4 % / Biso Wilson estimate: 28.75 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rpim(I) all: 0.1352 / Net I/σ(I): 12.18
Reflection shellResolution: 2.06→2.134 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 1.77 / Num. unique obs: 9686 / CC1/2: 0.691 / CC star: 0.904 / Rpim(I) all: 0.4555 / % possible all: 97.87

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
MxCuBEdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→48.79 Å / SU ML: 0.2135 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.4709
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2156 5007 5 %
Rwork0.1724 95183 -
obs0.1745 100190 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.12 Å2
Refinement stepCycle: LAST / Resolution: 2.06→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10425 0 210 868 11503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810891
X-RAY DIFFRACTIONf_angle_d0.966914801
X-RAY DIFFRACTIONf_chiral_restr0.05821746
X-RAY DIFFRACTIONf_plane_restr0.0061852
X-RAY DIFFRACTIONf_dihedral_angle_d8.83411467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.080.35721300.32962482X-RAY DIFFRACTION78.58
2.08-2.10.26941650.25933123X-RAY DIFFRACTION100
2.1-2.130.28211670.2373181X-RAY DIFFRACTION99.94
2.13-2.160.26691660.22943154X-RAY DIFFRACTION99.97
2.16-2.180.29441670.22343172X-RAY DIFFRACTION99.91
2.18-2.210.27961670.21533162X-RAY DIFFRACTION99.97
2.21-2.250.23611650.20333141X-RAY DIFFRACTION100
2.25-2.280.2541680.19423180X-RAY DIFFRACTION99.97
2.28-2.310.22541650.18893136X-RAY DIFFRACTION99.97
2.31-2.350.22981680.18983204X-RAY DIFFRACTION100
2.35-2.390.24951660.18853147X-RAY DIFFRACTION99.94
2.39-2.440.2481670.19173182X-RAY DIFFRACTION100
2.44-2.480.26391680.17973179X-RAY DIFFRACTION100
2.48-2.530.22651650.17943147X-RAY DIFFRACTION99.97
2.53-2.590.25241680.17953183X-RAY DIFFRACTION100
2.59-2.650.24281690.18493208X-RAY DIFFRACTION100
2.65-2.720.22481640.18173146X-RAY DIFFRACTION99.97
2.72-2.790.24251680.18093180X-RAY DIFFRACTION100
2.79-2.870.23721680.18563206X-RAY DIFFRACTION99.97
2.87-2.960.22391680.18073182X-RAY DIFFRACTION100
2.96-3.070.24131680.18013194X-RAY DIFFRACTION100
3.07-3.190.25811680.17433195X-RAY DIFFRACTION100
3.19-3.340.20071690.17163213X-RAY DIFFRACTION100
3.34-3.510.20121700.1613216X-RAY DIFFRACTION100
3.51-3.730.20151690.16413210X-RAY DIFFRACTION100
3.73-4.020.1821690.14753227X-RAY DIFFRACTION100
4.02-4.430.15951720.13113252X-RAY DIFFRACTION100
4.43-5.070.15571710.13113251X-RAY DIFFRACTION100
5.07-6.380.20611730.16283303X-RAY DIFFRACTION100
6.38-48.790.17321790.15933427X-RAY DIFFRACTION99.5

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