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- PDB-7dbk: Crystal structure of human LDHB in complex with NADH -

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Basic information

Entry
Database: PDB / ID: 7dbk
TitleCrystal structure of human LDHB in complex with NADH
ComponentsL-lactate dehydrogenase B chain
KeywordsOXIDOREDUCTASE / Lactate dehydrogenase / Inhibitor / Complex
Function / homology
Function and homology information


oxidoreductase complex / lactate metabolic process / Pyruvate metabolism / L-lactate dehydrogenase / L-lactate dehydrogenase activity / NAD metabolic process / pyruvate metabolic process / kinase binding / NAD binding / mitochondrial inner membrane ...oxidoreductase complex / lactate metabolic process / Pyruvate metabolism / L-lactate dehydrogenase / L-lactate dehydrogenase activity / NAD metabolic process / pyruvate metabolic process / kinase binding / NAD binding / mitochondrial inner membrane / membrane raft / mitochondrion / extracellular exosome / membrane / identical protein binding / cytosol / cytoplasm
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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / L-lactate dehydrogenase B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsSogabe, S. / Miwa, M.
CitationJournal: Sci Rep / Year: 2021
Title: Identification of the first highly selective inhibitor of human lactate dehydrogenase B.
Authors: Shibata, S. / Sogabe, S. / Miwa, M. / Fujimoto, T. / Takakura, N. / Naotsuka, A. / Kitamura, S. / Kawamoto, T. / Soga, T.
History
DepositionOct 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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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
E: L-lactate dehydrogenase B chain
F: 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)299,73538
Polymers292,3868
Non-polymers7,35030
Water17,601977
1
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)150,14422
Polymers146,1934
Non-polymers3,95118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28660 Å2
ΔGint-153 kcal/mol
Surface area45830 Å2
MethodPISA
2
E: L-lactate dehydrogenase B chain
F: 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)149,59116
Polymers146,1934
Non-polymers3,39912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27460 Å2
ΔGint-154 kcal/mol
Surface area45340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.477, 84.173, 156.210
Angle α, β, γ (deg.)90.000, 120.760, 90.000
Int Tables number5
Space group name H-MC121

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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: 36548.207 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDHB / Production host: Escherichia coli (E. coli) / References: UniProt: P07195, L-lactate dehydrogenase
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 977 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350, ammonium acetate, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 237609 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 0.994 / Rpim(I) all: 0.042 / Rsym value: 0.065 / Net I/σ(I): 19.8
Reflection shellResolution: 1.8→1.83 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 11881 / CC1/2: 0.736 / Rpim(I) all: 0.324 / Rsym value: 0.511 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I0Z

1i0z


Resolution: 1.802→49.993 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.666 / SU ML: 0.088 / Cross valid method: FREE R-VALUE / ESU R: 0.125 / ESU R Free: 0.116
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2034 11844 4.985 %
Rwork0.1702 225765 -
all0.172 --
obs-237609 99.487 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.333 Å2
Baniso -1Baniso -2Baniso -3
1--0.578 Å2-0 Å2-0.04 Å2
2--0.336 Å2-0 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.802→49.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20488 0 484 977 21949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01321310
X-RAY DIFFRACTIONr_bond_other_d0.0010.01720900
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.62628918
X-RAY DIFFRACTIONr_angle_other_deg1.3731.58148284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6152656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57224.771872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82153856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6121564
X-RAY DIFFRACTIONr_chiral_restr0.0770.22856
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0223616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024216
X-RAY DIFFRACTIONr_nbd_refined0.20.24117
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.219568
X-RAY DIFFRACTIONr_nbtor_refined0.1570.210255
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.29639
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2969
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0660.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2570.227
X-RAY DIFFRACTIONr_nbd_other0.1940.2125
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1250.214
X-RAY DIFFRACTIONr_mcbond_it1.0151.67210648
X-RAY DIFFRACTIONr_mcbond_other1.0151.67210647
X-RAY DIFFRACTIONr_mcangle_it1.6642.50213296
X-RAY DIFFRACTIONr_mcangle_other1.6642.50313297
X-RAY DIFFRACTIONr_scbond_it1.4141.93710662
X-RAY DIFFRACTIONr_scbond_other1.4141.93710663
X-RAY DIFFRACTIONr_scangle_it2.2222.82215622
X-RAY DIFFRACTIONr_scangle_other2.2222.82215623
X-RAY DIFFRACTIONr_lrange_it4.36920.51923209
X-RAY DIFFRACTIONr_lrange_other4.36720.50623199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.802-1.8490.2698500.23816434X-RAY DIFFRACTION98.1711
1.849-1.8990.2438310.21716278X-RAY DIFFRACTION99.9474
1.899-1.9550.2357870.20515899X-RAY DIFFRACTION99.9641
1.955-2.0150.2318340.18515368X-RAY DIFFRACTION100
2.015-2.0810.2117550.1814920X-RAY DIFFRACTION99.9936
2.081-2.1540.2027500.16714448X-RAY DIFFRACTION100
2.154-2.2350.227540.16813946X-RAY DIFFRACTION99.9932
2.235-2.3260.2037150.16313371X-RAY DIFFRACTION99.9787
2.326-2.430.2146820.16412887X-RAY DIFFRACTION99.9632
2.43-2.5480.2036260.1612332X-RAY DIFFRACTION99.9152
2.548-2.6860.2056110.16111740X-RAY DIFFRACTION99.9676
2.686-2.8490.2115940.16811020X-RAY DIFFRACTION99.8281
2.849-3.0450.2245520.16610384X-RAY DIFFRACTION99.7446
3.045-3.2890.2034910.1629690X-RAY DIFFRACTION99.2203
3.289-3.6030.1915010.1618836X-RAY DIFFRACTION99.0453
3.603-4.0280.1864400.1617999X-RAY DIFFRACTION98.437
4.028-4.650.1653640.156926X-RAY DIFFRACTION96.4924
4.65-5.6940.1893390.1755916X-RAY DIFFRACTION97.7344
5.694-8.0450.212380.1854727X-RAY DIFFRACTION99.3199
8.045-49.9930.1871300.1782644X-RAY DIFFRACTION97.6417
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6060.1372-0.1050.73580.06750.6407-0.0420.1031-0.0018-0.08820.0606-0.0412-0.04030.0031-0.01860.0179-0.01980.00190.03530.00480.00651.2255.668237.0714
20.9208-0.1342-0.10150.59170.09560.6773-0.00850.1399-0.0185-0.07890.00170.00260.0267-0.07460.00670.0412-0.04180.02270.0702-0.03340.028856.636524.298630.8741
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA2 - 334
2X-RAY DIFFRACTION1ALLB2 - 334
3X-RAY DIFFRACTION1ALLC2 - 334
4X-RAY DIFFRACTION1ALLD2 - 334
5X-RAY DIFFRACTION2ALLE2 - 334
6X-RAY DIFFRACTION2ALLF2 - 334
7X-RAY DIFFRACTION2ALLG2 - 334
8X-RAY DIFFRACTION2ALLH2 - 334

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