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- PDB-1q7i: Structural Analysis of Integrin alpha IIb beta 3- Disintegrin wit... -

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Basic information

Entry
Database: PDB / ID: 1q7i
TitleStructural Analysis of Integrin alpha IIb beta 3- Disintegrin with the AKGDWN Motif
ComponentsHemorrhagic protein-rhodostomin
KeywordsBLOOD CLOTTING / HYDROLASE / disintegrin / integrin / rhodostomin
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Disintegrin domain / Echistatin / Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. ...Disintegrin domain / Echistatin / Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Zinc metalloproteinase/disintegrin
Similarity search - Component
Biological speciesCalloselasma rhodostoma (Malayan pit viper)
MethodSOLUTION NMR / Hybrid distance geometry-dynamical simulated annealing method
AuthorsChuang, W.J. / Chen, C.Y. / Shiu, J.H. / Chen, Y.C.
CitationJournal: To be Published
Title: Structure Analysis of Integrin alpha IIb beta 3 - Specific Disintegrin with the ARGDWN Motif
Authors: Chuang, W.J. / Chen, C.Y. / Shiu, J.H. / Chen, Y.C.
History
DepositionAug 19, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemorrhagic protein-rhodostomin


Theoretical massNumber of molelcules
Total (without water)7,3871
Polymers7,3871
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #5fewest violations, lowest energy

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Components

#1: Protein Hemorrhagic protein-rhodostomin / Disintegrin kistrin / Platelet aggregation activation inhibitor


Mass: 7387.327 Da / Num. of mol.: 1 / Fragment: Disintegrin rhodostomin / Mutation: P48A/M52W/P53N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Calloselasma rhodostoma (Malayan pit viper)
Gene: RHOD / Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) / Strain (production host): X-33
References: UniProt: P30403, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1333D 15N-separated NOESY
1433D 15N-separated TOCSY
153HNHA
16315N-HSQC
1722D NOESY
1822D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
13mM Rhodostomin90% H2O/10% D2O
23mM Rhodostomin100% D2O
32.5mM U-15N90% H2O/10% D2O
Sample conditionsIonic strength: 0 / pH: 6 / Pressure: ambient / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukerprocessing
AURELIA2.7.10Neidigdata analysis
X-PLOR3.85Brungerrefinement
RefinementMethod: Hybrid distance geometry-dynamical simulated annealing method
Software ordinal: 1
NMR representativeSelection criteria: fewest violations, lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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