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- PDB-7dbj: Crystal structure of human LDHB in complex with NADH, oxamate, an... -

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Basic information

Entry
Database: PDB / ID: 7dbj
TitleCrystal structure of human LDHB in complex with NADH, oxamate, and AXKO-0046
ComponentsL-lactate dehydrogenase B chain
KeywordsOXIDOREDUCTASE / Lactate dehydrogenase / Inhibitor / Complex
Function / homology
Function and homology information


L-lactate dehydrogenase / oxidoreductase complex / NAD metabolic process / Pyruvate metabolism / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / kinase binding / NAD binding / mitochondrial inner membrane ...L-lactate dehydrogenase / oxidoreductase complex / NAD metabolic process / Pyruvate metabolism / lactate metabolic process / L-lactate dehydrogenase activity / 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
Chem-H1U / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / OXAMIC ACID / L-lactate dehydrogenase B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.551 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,39621
Polymers146,1934
Non-polymers4,20417
Water13,781765
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20440 Å2
ΔGint-119 kcal/mol
Surface area44750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.389, 137.577, 84.909
Angle α, β, γ (deg.)90.000, 109.264, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#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.: 4
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

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Non-polymers , 5 types, 782 molecules

#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical
ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H3NO3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-H1U / N-[[3-[2-[(phenylmethyl)amino]ethyl]-1H-indol-2-yl]methyl]cycloheptanamine


Mass: 375.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H33N3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 765 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350, potassium formate, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 183405 / % possible obs: 99.2 % / Redundancy: 4.1 % / CC1/2: 0.989 / Rpim(I) all: 0.042 / Rsym value: 0.076 / Net I/σ(I): 20.3
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 4 / Num. unique obs: 8628 / CC1/2: 0.923 / Rpim(I) all: 0.149 / Rsym value: 0.251 / % possible all: 93.8

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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: 1.551→43.496 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.83 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.08 / ESU R Free: 0.077
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1917 9146 4.988 %
Rwork0.1697 174218 -
all0.171 --
obs-183364 98.923 %
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: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.534 Å20 Å20.232 Å2
2--0.049 Å2-0 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.551→43.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10244 0 284 765 11293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01310715
X-RAY DIFFRACTIONr_bond_other_d0.0110.01710502
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.63514543
X-RAY DIFFRACTIONr_angle_other_deg1.61.59124258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41851334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14424.636440
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.576104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.901151931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5081532
X-RAY DIFFRACTIONr_chiral_restr0.0830.21431
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211971
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022157
X-RAY DIFFRACTIONr_nbd_refined0.2080.22048
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.29832
X-RAY DIFFRACTIONr_nbtor_refined0.1630.25256
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.24726
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2582
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1770.220
X-RAY DIFFRACTIONr_nbd_other0.2630.281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.219
X-RAY DIFFRACTIONr_mcbond_it0.6421.85330
X-RAY DIFFRACTIONr_mcbond_other0.641.85329
X-RAY DIFFRACTIONr_mcangle_it0.8062.6996657
X-RAY DIFFRACTIONr_mcangle_other0.8062.6996658
X-RAY DIFFRACTIONr_scbond_it0.9691.9495385
X-RAY DIFFRACTIONr_scbond_other0.9691.955386
X-RAY DIFFRACTIONr_scangle_it1.2472.8857883
X-RAY DIFFRACTIONr_scangle_other1.2472.8867884
X-RAY DIFFRACTIONr_lrange_it3.06522.2211893
X-RAY DIFFRACTIONr_lrange_other3.05822.14111861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.551-1.5910.2336320.20411885X-RAY DIFFRACTION91.3183
1.591-1.6350.2366190.18812477X-RAY DIFFRACTION98.4292
1.635-1.6820.2176380.18512259X-RAY DIFFRACTION99.223
1.682-1.7340.2066040.18511854X-RAY DIFFRACTION99.3144
1.734-1.7910.2086220.18611521X-RAY DIFFRACTION99.3861
1.791-1.8540.2076040.18511177X-RAY DIFFRACTION99.4681
1.854-1.9240.2065350.17910784X-RAY DIFFRACTION99.6215
1.924-2.0020.2095160.18210422X-RAY DIFFRACTION99.8175
2.002-2.0910.2095430.1799949X-RAY DIFFRACTION99.7908
2.091-2.1930.2095060.1729567X-RAY DIFFRACTION99.7129
2.193-2.3120.1914590.1699054X-RAY DIFFRACTION99.8531
2.312-2.4520.1974660.1698602X-RAY DIFFRACTION99.8788
2.452-2.6210.194170.1678085X-RAY DIFFRACTION99.8473
2.621-2.8310.1954120.1747536X-RAY DIFFRACTION99.774
2.831-3.1010.1833880.1696875X-RAY DIFFRACTION99.945
3.101-3.4660.2013430.1716283X-RAY DIFFRACTION99.9095
3.466-4.0010.1882970.1645507X-RAY DIFFRACTION99.7765
4.001-4.8970.1612620.1434704X-RAY DIFFRACTION99.9195
4.897-6.9130.1821820.1653628X-RAY DIFFRACTION99.8166
6.913-43.4960.1411010.1612051X-RAY DIFFRACTION99.262
Refinement TLS params.Method: refined / Origin x: 14.8998 Å / Origin y: -0.0812 Å / Origin z: 6.9512 Å
111213212223313233
T0.0117 Å20.0045 Å20.0029 Å2-0.0064 Å20.004 Å2--0.003 Å2
L0.3641 °20.0303 °2-0.0195 °2-0.6172 °20.0165 °2--0.1492 °2
S-0.0108 Å °-0.0378 Å °-0.0286 Å °0.0628 Å °0.0082 Å °0.0003 Å °0.0101 Å °-0.0071 Å °0.0026 Å °
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

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