Macromolecule Content

• Total Structure Weight: 1460.78 
• Atom Count: 101 
• Residue Count: 13 
• Unique protein chains: 1

1I93

NMR ENSEMBLE OF ION-SELECTIVE LIGAND D16 FOR PLATELET INTEGRIN ALPHAIIB-BETA3

• DOI: 10.2210/pdb1I93/pdb

• Classification: CELL ADHESION


• Deposited: 2001-03-17 Released: 2002-07-10 
• Deposition Author(s): Smith, J.W., Le Calvez, H., Parra-Gessert, L., Preece, N.E., Jia, X., Assa-Munt, N.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Literature

Selection and structure of ion-selective ligands for platelet integrin alpha IIb(beta) 3.

Smith, J.W., Le Calvez, H., Parra-Gessert, L., Preece, N.E., Jia, X., Assa-Munt, N.

(2002) J.Biol.Chem. 277: 10298-10305

• PubMed: 11748219 
• DOI: 10.1074/jbc.M108071200
• Primary Citation of Related Structures:  
  1I98, 1I8E, 1I6Y


• PubMed Abstract: 
  

Integrins contain a number of divalent cation binding sites that control ligand binding affinity. Ions such as Ca(2+) and Mg(2+) bind to distinct sites on integrin and can have opposing effects on ligand binding. These effects are presumably brought about by alterations of the shape of the ligand binding pocket. To gain insight into the nature of these structural differences, we probed the integrin ligand binding site with an RGD-based library of unparalleled complexity. A cysteine-constrained phage library containing six random amino acids and the RGD motif present in seven different registers was used to select for ligands that exhibit ion-selective binding to integrin alpha(IIb)beta(3). The library was used to select for peptides that bind to the integrin alpha(IIb)beta(3) preferentially in Ca(2+) versus Mg(2+). Peptides were identified which bound selectively in each ion. The Ca(2+)-selective peptides had a range of sequences, with the only obvious consensus involving a motif that had four cysteine residues bonded in a 1,4:2,3 arrangement. Interestingly though, the Mg(2+)-selective peptides exhibited a well defined consensus motif containing Cys-X-aromatic-L/G-R-G-D-hydrophobic-R-R/K-Cys. As a first step toward understanding the structural basis for this selectivity, solution NMR structures were obtained for representatives of both sets of peptides. All peptides formed turns, with the RGD motif at the apex. The Mg(2+)-selected peptides contained a unique basic patch that protrudes from the base of the turn.

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Organizational Affiliation: 

Program on Cell Adhesion, Cancer Research Center, the Burnham Institute, La Jolla, California 92037, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ION-SELECTIVE LIGAND D16	A	13	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NH2	A	NON-POLYMER	H2 N		--
ACE	A	NON-POLYMER	C2 H4 O		--

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 
• Olderado: 1I93 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-03-17 
• Released Date: 2002-07-10 
• Deposition Author(s): Smith, J.W., Le Calvez, H., Parra-Gessert, L., Preece, N.E., Jia, X., Assa-Munt, N.

Revision History 

• Version 1.0: 2002-07-10
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance