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- PDB-4bv5: Identification of small molecule inhibitors selective for apo(a) ... -

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Basic information

Entry
Database: PDB / ID: 4bv5
TitleIdentification of small molecule inhibitors selective for apo(a) kringles KIV-7, KIV-10 and KV.
ComponentsAPOLIPOPROTEIN(A)
KeywordsHYDROLASE / CARDIOVASCULAR DISEASE / OPTICAL BIOSENSORS
Function / homology
Function and homology information


plasma lipoprotein particle / LDL remodeling / blood circulation / lipid transport / endopeptidase inhibitor activity / apolipoprotein binding / fibronectin binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / lipid metabolic process / heparin binding ...plasma lipoprotein particle / LDL remodeling / blood circulation / lipid transport / endopeptidase inhibitor activity / apolipoprotein binding / fibronectin binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / lipid metabolic process / heparin binding / serine-type endopeptidase activity / extracellular region
Similarity search - Function
Plasminogen Kringle 4 / Plasminogen Kringle 4 / Kringle domain / Kringle domain signature. / Kringle domain / Kringle / Kringle domain profile. / Kringle superfamily / Kringle, conserved site / Kringle-like fold ...Plasminogen Kringle 4 / Plasminogen Kringle 4 / Kringle domain / Kringle domain signature. / Kringle domain / Kringle / Kringle domain profile. / Kringle superfamily / Kringle, conserved site / 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 domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-5C3 / Apolipoprotein(a)
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSandmark, J. / Althage, M. / Andersson, G.M.K. / Antonsson, T. / Blaho, S. / Bodin, C. / Bostrom, J. / Chen, Y. / Dahlen, A. / Eriksson, P.O. ...Sandmark, J. / Althage, M. / Andersson, G.M.K. / Antonsson, T. / Blaho, S. / Bodin, C. / Bostrom, J. / Chen, Y. / Dahlen, A. / Eriksson, P.O. / Evertsson, E. / Fex, T. / Fjellstrom, O. / Gustafsson, D. / Hallberg, C. / Hicks, R. / Jarkvist, E. / Johansson, C. / Kalies, I. / Kang, D. / Svalstedt Karlsson, B. / Kartberg, F. / Legnehed, A. / Lindqvist, A.M. / Martinsson, S.A. / Moberg, A. / Petersson, A.U. / Ridderstrom, M. / Thelin, A. / Tigerstrom, A. / Vinblad, J. / Xu, B. / Knecht, W.
CitationJournal: To be Published
Title: Small Molecules Used to Decipher the Pathophysiological Roles of the Kringle Domains Kiv-7, - 10 and Kv of Apolipoprotein(A)
Authors: Sandmark, J. / Althage, M. / Andersson, G.M.K. / Antonsson, T. / Blaho, S. / Bodin, C. / Bostrom, J. / Chen, Y. / Dahlen, A. / Eriksson, P.O. / Evertsson, E. / Fex, T. / Fjellstrom, O. / ...Authors: Sandmark, J. / Althage, M. / Andersson, G.M.K. / Antonsson, T. / Blaho, S. / Bodin, C. / Bostrom, J. / Chen, Y. / Dahlen, A. / Eriksson, P.O. / Evertsson, E. / Fex, T. / Fjellstrom, O. / Gustafsson, D. / Hallberg, C. / Hicks, R. / Jarkvist, E. / Johansson, C. / Kalies, I. / Kang, D. / Svalstedt Karlsson, B. / Kartberg, F. / Legnehed, A. / Lindqvist, A.M. / Martinsson, S.A. / Moberg, A. / Petersson, A.U. / Ridderstrom, M. / Thelin, A. / Tigerstrom, A. / Vinblad, J. / Xu, B. / Knecht, W.
History
DepositionJun 25, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APOLIPOPROTEIN(A)
B: APOLIPOPROTEIN(A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9054
Polymers18,3122
Non-polymers5932
Water1,02757
1
A: APOLIPOPROTEIN(A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4522
Polymers9,1561
Non-polymers2961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: APOLIPOPROTEIN(A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4522
Polymers9,1561
Non-polymers2961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)24.410, 45.250, 56.100
Angle α, β, γ (deg.)90.00, 90.67, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9999, 9.8E-5, 0.01379), (9.6E-5, -1, 0.000151), (0.01379, -0.00015, -0.9999)
Vector: 11.9017, 25.7049, 28.1256)

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Components

#1: Protein APOLIPOPROTEIN(A) / APO(A) / LP(A)


Mass: 9156.078 Da / Num. of mol.: 2 / Fragment: KRINGLE IV-10, RESIDUES 4123-4201 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPICZALPHA / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): X-33
References: UniProt: P08519, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-5C3 / 4-(aminomethyl)-N-(benzenesulfonyl)cyclohexanecarboxamide


Mass: 296.385 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N2O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsKRINGLE IV-10 DOMAIN, N76A MUTATION

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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: 1.7 Å3/Da / Density % sol: 29 % / Description: NONE
Crystal growpH: 4.6 / Details: 30% PEG400, 0.1M CACL2, 0.1M NAOAC PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ / Wavelength: 1.5418
DetectorType: RIGAKU A200-CU / Detector: CCD / Date: Oct 4, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→28 Å / Num. obs: 6931 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 5.9
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.8 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KIV
Resolution: 2.1→28.06 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.896 / Cross valid method: THROUGHOUT / ESU R: 0.526 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23013 314 4.7 %RANDOM
Rwork0.18986 ---
obs0.19187 6303 91.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.524 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å2-0.31 Å2
2---0.88 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 40 57 1355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191351
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.9411843
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4635152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.21522.17469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.31515186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1131514
X-RAY DIFFRACTIONr_chiral_restr0.0910.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211098
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 21 -
Rwork0.288 416 -
obs--81.53 %

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