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- PDB-1drs: THREE-DIMENSIONAL STRUCTURE OF THE RGD-CONTAINING NEUROTOXIN HOMO... -

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Basic information

Entry
Database: PDB / ID: 1drs
TitleTHREE-DIMENSIONAL STRUCTURE OF THE RGD-CONTAINING NEUROTOXIN HOMOLOGUE, DENDROASPIN
ComponentsDENDROASPIN
KeywordsCELL ADHESION PROTEIN
Function / homologySnake three-finger toxin / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / toxin activity / extracellular region / Mainly Beta / Dendroaspin
Function and homology information
Biological speciesDendroaspis jamesoni kaimosae (eastern Jameson's mamba)
MethodSOLUTION NMR
AuthorsSutcliffe, M.J. / Jaseja, M. / Hyde, E.I. / Lu, X. / Williams, J.A.
Citation
Journal: Nat.Struct.Biol. / Year: 1994
Title: Three-dimensional structure of the RGD-containing neurotoxin homologue dendroaspin.
Authors: Sutcliffe, M.J. / Jaseja, M. / Hyde, E.I. / Lu, X. / Williams, J.A.
#1: Journal: To be Published
Title: 1H NMR Assignments and Secondary Structure of Dendroaspin, an Rgd-Containing Glycoprotein Iibiiia (Alphaiib-Beta3) Antagonist with a Neurotoxin Fold
Authors: Jaseja, M. / Lu, X. / Williams, J.A. / Sutcliffe, M.J. / Kakkar, V.V. / Parslow, R.A. / Hyde, E.I.
History
DepositionSep 29, 1994Processing site: BNL
Revision 1.0Dec 20, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name
Revision 1.4Oct 30, 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: DENDROASPIN


Theoretical massNumber of molelcules
Total (without water)6,7621
Polymers6,7621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: ASN 25 - ILE 26 MODEL 2 OMEGA = 210.86 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: ARG 34 - ARG 35 MODEL 2 OMEGA = 217.58 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: ASN 25 - ILE 26 MODEL 5 OMEGA = 212.10 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: ARG 34 - ARG 35 MODEL 5 OMEGA = 213.53 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: ARG 34 - ARG 35 MODEL 12 OMEGA = 213.81 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
6: ASN 25 - ILE 26 MODEL 20 OMEGA = 211.78 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: ARG 34 - ARG 35 MODEL 20 OMEGA = 211.83 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
8: ARG 34 - ARG 35 MODEL 29 OMEGA = 211.54 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
9: ASN 25 - ILE 26 MODEL 30 OMEGA = 210.43 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
10: ARG 34 - ARG 35 MODEL 34 OMEGA = 210.60 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
11: ASN 25 - ILE 26 MODEL 35 OMEGA = 211.83 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
12: ASN 25 - ILE 26 MODEL 36 OMEGA = 212.94 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)39 / -
Representative

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Components

#1: Protein DENDROASPIN


Mass: 6761.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendroaspis jamesoni kaimosae (eastern Jameson's mamba)
Species: Dendroaspis jamesoni / Strain: kaimosae / References: UniProt: P28375
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Processing

NMR software
NameDeveloperClassification
DiscoverBIOSYM TECHNOLOGIES INC.refinement
DGIIHAVELrefinement
NMR ensembleConformers submitted total number: 39

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