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- PDB-8v8z: Lipoprotein(a) Kringle IV domain 8 - Lp(a) KIV8 in complex with L... -

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Basic information

Entry
Database: PDB / ID: 8v8z
TitleLipoprotein(a) Kringle IV domain 8 - Lp(a) KIV8 in complex with LY3473329
ComponentsApolipoprotein(a)
KeywordsLIPID BINDING PROTEIN / Complex / Inhibitor / LDL
Function / homology
Function and homology information


plasma lipoprotein particle / LDL remodeling / blood circulation / lipid transport / endopeptidase inhibitor activity / apolipoprotein binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / fibronectin binding / lipid metabolic process / heparin binding ...plasma lipoprotein particle / LDL remodeling / blood circulation / lipid transport / endopeptidase inhibitor activity / apolipoprotein binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / fibronectin binding / lipid metabolic process / heparin binding / endopeptidase activity / serine-type endopeptidase activity / signaling receptor binding / proteolysis / extracellular space / extracellular region
Similarity search - Function
: / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Serine proteases, trypsin family, histidine active site ...: / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
: / Apolipoprotein(a)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsHendle, J. / Weichert, K. / Sauder, J.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2024
Title: Discovery of potent small-molecule inhibitors of lipoprotein(a) formation.
Authors: Diaz, N. / Perez, C. / Escribano, A.M. / Sanz, G. / Priego, J. / Lafuente, C. / Barberis, M. / Calle, L. / Espinosa, J.F. / Priest, B.T. / Zhang, H.Y. / Nosie, A.K. / Haas, J.V. / Cannady, E. ...Authors: Diaz, N. / Perez, C. / Escribano, A.M. / Sanz, G. / Priego, J. / Lafuente, C. / Barberis, M. / Calle, L. / Espinosa, J.F. / Priest, B.T. / Zhang, H.Y. / Nosie, A.K. / Haas, J.V. / Cannady, E. / Borel, A. / Schultze, A.E. / Sauder, J.M. / Hendle, J. / Weichert, K. / Nicholls, S.J. / Michael, L.F.
History
DepositionDec 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apolipoprotein(a)
B: Apolipoprotein(a)
C: Apolipoprotein(a)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4054
Polymers32,6943
Non-polymers7111
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.755, 75.179, 93.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Apolipoprotein(a) / Apo(a) / Lp(a)


Mass: 10898.084 Da / Num. of mol.: 3 / Fragment: Kringle IV domain 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LPA / Production host: Escherichia coli (E. coli)
References: UniProt: P08519, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-A1AAK / muvalaplin / (2S,2'S,2''S)-3,3',3''-[azaniumyltris(methylene-3,1-phenylene)]tris{2-[(3R)-pyrrolidin-1-ium-3-yl]propanoate}


Mass: 710.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H54N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 30% PEG 300, 100mM Sodium Acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.01→35 Å / Num. obs: 18167 / % possible obs: 99.3 % / Redundancy: 7.3 % / CC1/2: 0.997 / Net I/σ(I): 14.1
Reflection shellResolution: 2.01→2.12 Å / Redundancy: 7.5 % / Num. unique obs: 2580 / CC1/2: 0.929 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.905 / SU B: 5.451 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25973 869 4.8 %RANDOM
Rwork0.21689 ---
obs0.21898 17292 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å2-0 Å2-0 Å2
2---2.95 Å20 Å2
3---2.12 Å2
Refinement stepCycle: LAST / Resolution: 2.01→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 52 88 2116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192131
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.9072918
X-RAY DIFFRACTIONr_angle_other_deg0.8323135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1995244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.17520.381105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4615306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.061531
X-RAY DIFFRACTIONr_chiral_restr0.0810.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211683
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0212
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3458.097961
X-RAY DIFFRACTIONr_mcbond_other3.3448.103962
X-RAY DIFFRACTIONr_mcangle_it4.53912.0821199
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2589.0451170
X-RAY DIFFRACTIONr_scbond_other4.2569.0421171
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.77913.2081716
X-RAY DIFFRACTIONr_long_range_B_refined7.63639.1863342
X-RAY DIFFRACTIONr_long_range_B_other7.57139.193326
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 75 -
Rwork0.285 1235 -
obs--100 %

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