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- PDB-8s88: Crystal structure of human L-lactate Dehydrogenase B protein in c... -

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Basic information

Entry
Database: PDB / ID: 8s88
TitleCrystal structure of human L-lactate Dehydrogenase B protein in complex with NADH, oxamate and fluoxetine
ComponentsL-lactate dehydrogenase B chain
KeywordsOXIDOREDUCTASE / Complex / Fluoxetine
Function / homology
Function and homology information


L-lactate dehydrogenase / oxidoreductase complex / L-lactate dehydrogenase (NAD+) activity / NAD+ metabolic process / Pyruvate metabolism / lactate metabolic process / pyruvate metabolic process / kinase binding / NAD binding / mitochondrial inner membrane ...L-lactate dehydrogenase / oxidoreductase complex / L-lactate dehydrogenase (NAD+) activity / NAD+ metabolic process / Pyruvate metabolism / lactate metabolic process / pyruvate metabolic process / kinase binding / NAD binding / mitochondrial inner membrane / membrane raft / mitochondrion / extracellular exosome / identical protein binding / membrane / cytosol / cytoplasm
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 / DI(HYDROXYETHYL)ETHER / Chem-SFX / L-lactate dehydrogenase B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsVan Gysel, M. / Wouters, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS) Belgium
CitationJournal: To Be Published
Title: Crystal structure of human L-lactate Dehydrogenase B protein in complex with NADH, oxamate and fluoxetine
Authors: Van Gysel, M. / Wouters, J.
History
DepositionMar 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
E: L-lactate dehydrogenase B chain
F: L-lactate dehydrogenase B chain
G: L-lactate dehydrogenase B chain
H: L-lactate dehydrogenase B chain
I: L-lactate dehydrogenase B chain
J: L-lactate dehydrogenase B chain
K: L-lactate dehydrogenase B chain
L: L-lactate dehydrogenase B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)478,73185
Polymers463,22912
Non-polymers15,50173
Water24,0861337
1
A: L-lactate dehydrogenase B chain
B: L-lactate dehydrogenase B chain
G: L-lactate dehydrogenase B chain
H: L-lactate dehydrogenase B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,79830
Polymers154,4104
Non-polymers5,38826
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29700 Å2
ΔGint-218 kcal/mol
Surface area42970 Å2
MethodPISA
2
C: L-lactate dehydrogenase B chain
D: L-lactate dehydrogenase B chain
hetero molecules

F: L-lactate dehydrogenase B chain
I: L-lactate dehydrogenase B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,83128
Polymers154,4104
Non-polymers5,42124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area30000 Å2
ΔGint-205 kcal/mol
Surface area43350 Å2
MethodPISA
3
E: L-lactate dehydrogenase B chain
K: L-lactate dehydrogenase B chain
hetero molecules

J: L-lactate dehydrogenase B chain
hetero molecules

L: L-lactate dehydrogenase B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,10127
Polymers154,4104
Non-polymers4,69223
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area29870 Å2
ΔGint-219 kcal/mol
Surface area42260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.530, 413.960, 85.300
Angle α, β, γ (deg.)90.000, 109.570, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

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


Mass: 38602.441 Da / Num. of mol.: 12
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

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Non-polymers , 8 types, 1410 molecules

#2: Chemical
ChemComp-SFX / (3S)-N-methyl-3-phenyl-3-[4-(trifluoromethyl)phenoxy]propan-1-amine / Fluoxetine


Mass: 309.326 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C17H18F3NO / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antidepressant, inhibitor*YM
#3: Chemical
ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1337 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis-Tris pH 5.5, 25% (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: Oct 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.07→48.67 Å / Num. obs: 259434 / % possible obs: 99.35 % / Redundancy: 7.1 % / Biso Wilson estimate: 34.37 Å2 / CC1/2: 0.956 / CC star: 0.989 / Net I/σ(I): 9.23
Reflection shellResolution: 2.07→2.149 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 25018 / CC1/2: 0.778 / CC star: 0.936

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
MxCuBEdata collection
Coot0.9.4.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→48.67 Å / SU ML: 0.2983 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.4555
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2638 12943 5 %
Rwork0.2129 245920 -
obs0.2156 258864 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.39 Å2
Refinement stepCycle: LAST / Resolution: 2.07→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30744 0 1017 1337 33098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008532272
X-RAY DIFFRACTIONf_angle_d1.245343775
X-RAY DIFFRACTIONf_chiral_restr0.0585155
X-RAY DIFFRACTIONf_plane_restr0.00725410
X-RAY DIFFRACTIONf_dihedral_angle_d9.46824425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.10.39973640.33436892X-RAY DIFFRACTION84.43
2.1-2.120.36474360.31178271X-RAY DIFFRACTION99.6
2.12-2.150.38384320.3098238X-RAY DIFFRACTION99.75
2.15-2.180.3654310.29528174X-RAY DIFFRACTION99.71
2.18-2.20.36474310.29898201X-RAY DIFFRACTION99.76
2.2-2.230.33624340.27598247X-RAY DIFFRACTION99.72
2.23-2.270.33444280.26628163X-RAY DIFFRACTION99.79
2.27-2.30.30874390.25618343X-RAY DIFFRACTION99.68
2.3-2.340.33074280.26648122X-RAY DIFFRACTION99.87
2.34-2.370.33914370.26288303X-RAY DIFFRACTION99.79
2.37-2.420.35134300.26348181X-RAY DIFFRACTION99.93
2.42-2.460.33074350.26518258X-RAY DIFFRACTION99.85
2.46-2.510.33144330.25778206X-RAY DIFFRACTION99.85
2.51-2.560.30454350.2558281X-RAY DIFFRACTION99.7
2.56-2.610.32894300.25878161X-RAY DIFFRACTION99.81
2.61-2.670.32824360.25968277X-RAY DIFFRACTION99.94
2.67-2.740.32374330.25948222X-RAY DIFFRACTION99.99
2.74-2.820.33974330.26348243X-RAY DIFFRACTION99.99
2.82-2.90.2994370.24438301X-RAY DIFFRACTION99.99
2.9-2.990.30974310.23438188X-RAY DIFFRACTION99.97
2.99-3.10.30224340.23938233X-RAY DIFFRACTION100
3.1-3.220.30694350.23188280X-RAY DIFFRACTION100
3.22-3.370.26734350.21918266X-RAY DIFFRACTION100
3.37-3.550.23424370.19258284X-RAY DIFFRACTION99.99
3.55-3.770.2374320.18468219X-RAY DIFFRACTION99.99
3.77-4.060.20784360.17448279X-RAY DIFFRACTION99.99
4.06-4.470.19044360.15388287X-RAY DIFFRACTION100
4.47-5.110.19484330.15548251X-RAY DIFFRACTION99.97
5.11-6.440.22794340.17688247X-RAY DIFFRACTION99.97
6.44-48.670.18314380.16648302X-RAY DIFFRACTION99.69

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