1NYP Cell Adhesion date Feb 13, 2003
title 4th Lim Domain Of Pinch Protein
authors A.Velyvis, J.Vaynberg, O.Vinogradova, Y.Zhang, C.Wu, J.Qin
compound source
Molecule: Pinch Protein
Chain: A
Fragment: 4th Lim Domain
Synonym: Lim And Senescent Cell Antigen-Like Domains 1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lims1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-4t1
methodSolution NMR
ligand ZN enzyme
Primary referenceStructural and functional insights into PINCH LIM4 domain-mediated integrin signaling., Velyvis A, Vaynberg J, Yang Y, Vinogradova O, Zhang Y, Wu C, Qin J, Nat Struct Biol 2003 Jul;10(7):558-64. PMID:12794636
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (350 Kb) [Save to disk]
  • LPC: Ligand-Protein Contacts for 1NYP
  • CSU: Contacts of Structural Units for 1NYP
  • Original NMR restraints for 1NYP from PDB
  • Experimental data, such as chemical shifts, at BioMagResBank (BMRB)
  • NMR Restraints Grid from BioMagResBank (BMRB)
  • Retrieve 1NYP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NYP from S2C, [Save to disk]
  • View 1NYP in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1NYP
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1NYP, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nypa1, region A:1-31 [Jmol] [rasmolscript] [script source]
        - Domain d1nypa2, region A:32-66 [Jmol] [rasmolscript] [script source]
  • Fold representative 1nyp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1nyp_A] [1nyp]
  • SWISS-PROT database: [P48059]
  • Domain organization of [LIMS1_HUMAN] by SWISSPFAM
  • Domain found in 1NYP: [LIM ] by SMART
  • Other resources with information on 1NYP
  • Community annotation for 1NYP at PDBWiki (http://pdbwiki.org)
  • NMR Ensemble (OLDERADO: core, domain and representative structure database)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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