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- PDB-2adf: Crystal Structure and Paratope Determination of 82D6A3, an Antith... -

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Basic information

Entry
Database: PDB / ID: 2adf
TitleCrystal Structure and Paratope Determination of 82D6A3, an Antithrombotic Antibody Directed Against the von Willebrand factor A3-Domain
Components
  • (82D6A3 IgG) x 2
  • Von Willebrand factor
KeywordsBLOOD CLOTTING/IMMUNE SYSTEM / on Willebrand factor / A3-domain / 82D6A3 / collagen binding / paratope / epitope / antithrombotic / BLOOD CLOTTING-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / Weibel-Palade body / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen ...Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / Weibel-Palade body / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / immunoglobulin binding / immunoglobulin complex / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin cell surface interactions / immunoglobulin mediated immune response / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / antigen binding / Integrin signaling / extracellular matrix / platelet alpha granule lumen / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet activation / response to wounding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / blood coagulation / integrin binding / Platelet degranulation / protein-folding chaperone binding / protease binding / collagen-containing extracellular matrix / cell adhesion / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. ...von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / : / von Willebrand factor, type A domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / von Willebrand factor / Ig heavy chain Mem5 / :
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStaelens, S. / Hadders, M.A. / Vauterin, S. / Platteau, C. / Vanhoorelbeke, K. / Huizinga, E.G. / Deckmyn, H.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Paratope determination of the antithrombotic antibody 82D6A3 based on the crystal structure of its complex with the von Willebrand factor A3-domain
Authors: Staelens, S. / Hadders, M.A. / Vauterin, S. / Platteau, C. / De Maeyer, M. / Vanhoorelbeke, K. / Huizinga, E.G. / Deckmyn, H.
History
DepositionJul 20, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Von Willebrand factor
H: 82D6A3 IgG
L: 82D6A3 IgG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8807
Polymers67,5363
Non-polymers3444
Water7,963442
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.179, 89.076, 123.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Von Willebrand factor / vWF


Mass: 20790.697 Da / Num. of mol.: 1 / Fragment: A3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21 / References: UniProt: P04275

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Antibody , 2 types, 2 molecules HL

#2: Antibody 82D6A3 IgG


Mass: 23652.463 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Secretion: ascites / References: UniProt: P84751
#3: Antibody 82D6A3 IgG


Mass: 23092.590 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Secretion: ascites / References: UniProt: Q58EV6

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Non-polymers , 4 types, 446 molecules

#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O

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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: 3 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 8000, ammonium sulphate, acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.9→27.35 Å / Num. all: 63303 / Num. obs: 60060 / % possible obs: 100 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5
Reflection shellResolution: 1.9→2 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ATZ, 2MPA

1atz

2mpa


Resolution: 1.9→27.35 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.415 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 5 / σ(I): 5 / ESU R: 0.134 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21969 3243 5.1 %RANDOM
Rwork0.19095 ---
all0.19243 60060 --
obs0.19243 60060 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.253 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4703 0 20 442 5165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224831
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9456577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7215613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.90924.421190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82915779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8781520
X-RAY DIFFRACTIONr_chiral_restr0.0910.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023625
X-RAY DIFFRACTIONr_nbd_refined0.1940.22114
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23275
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2378
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.226
X-RAY DIFFRACTIONr_mcbond_it0.7921.53162
X-RAY DIFFRACTIONr_mcangle_it1.0224973
X-RAY DIFFRACTIONr_scbond_it1.60531939
X-RAY DIFFRACTIONr_scangle_it2.4254.51604
LS refinement shellResolution: 1.9→2.002 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.254 446 -
Rwork0.221 8662 -
obs--100 %

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