2SEM Signaling Protein Inhibitor date Nov 02, 1998
title Sem5 Sh3 Domain Complexed With Peptoid Inhibitor
authors J.T.Nguyen, C.W.Turck, F.E.Cohen, R.N.Zuckermann, W.A.Lim
compound source
Molecule: Protein (Sex Muscle Abnormal Protein 5)
Chain: A, B
Fragment: C-Terminal Sh3
Engineered: Yes
 Organism_scientific: Caenorhabditis Elegans
Organism_taxid: 6239
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Protein (Sh3 Peptoid Inhibitor)
Chain: C, D
Engineered: Yes
Synthetic: Yes
Other_details: Peptidomimetic Inhibitor
symmetry Space Group: P 1 21 1
R_factor 0.206 R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
33.200 59.900 33.600 90.00 102.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand ACE, IPG enzyme
related structures by homologous chain: 1SEM, 3SEM
Primary referenceExploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors., Nguyen JT, Turck CW, Cohen FE, Zuckermann RN, Lim WA, Science 1998 Dec 11;282(5396):2088-92. PMID:9851931
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (28 Kb) [Save to disk]
  • Biological Unit Coordinates (2sem.pdb1.gz) 24 Kb
  • LPC: Ligand-Protein Contacts for 2SEM
  • CSU: Contacts of Structural Units for 2SEM
  • Likely Quarternary Molecular Structure file(s) for 2SEM
  • Retrieve 2SEM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2SEM from S2C, [Save to disk]
    • View 2SEM 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 2SEM
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2SEM, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d2sema_, region A [Jmol] [rasmolscript] [script source]
        - Domain d2semb_, region B [Jmol] [rasmolscript] [script source]
  • 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: [2sem] [2sem_C] [2sem_A] [2sem_B] [2sem_D]
  • SWISS-PROT database: [P29355]
  • Domain organization of [SEM5_CAEEL] by SWISSPFAM
  • Domain found in 2SEM: [SH3 ] by SMART
    • Other resources with information on 2SEM
  • Community annotation for 2SEM at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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