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(-) Description

Title :  SEM5 SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR
 
Authors :  J. T. Nguyen, C. W. Turck, F. E. Cohen, R. N. Zuckermann, W. A. Lim
Date :  02 Nov 98  (Deposition) - 06 Jan 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Sh3 Domain, Inhibitors, Peptoids, Protein-Protein Recognition, Proline-Rich Motifs, Signal Transduction, Signaling Protein, Signaling Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. T. Nguyen, C. W. Turck, F. E. Cohen, R. N. Zuckermann, W. A. Lim
Exploiting The Basis Of Proline Recognition By Sh3 And Ww Domains: Design Of N-Substituted Inhibitors.
Science V. 282 2088 1998
PubMed-ID: 9851931  |  Reference-DOI: 10.1126/SCIENCE.282.5396.2088

(-) Compounds

Molecule 1 - PROTEIN (SEX MUSCLE ABNORMAL PROTEIN 5)
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentC-TERMINAL SH3
    Organism ScientificCAENORHABDITIS ELEGANS
    Organism Taxid6239
 
Molecule 2 - PROTEIN (SH3 PEPTOID INHIBITOR)
    ChainsC, D
    EngineeredYES
    Other DetailsPEPTIDOMIMETIC INHIBITOR
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2IPG2Mod. Amino AcidN-ISOPROPYL GLYCINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:163 , GLN A:168 , GLU A:172 , ASN A:190 , TRP A:191 , ASN A:206 , TYR A:207 , HOH C:10 , HOH C:11 , HOH C:12 , HOH C:13BINDING SITE FOR CHAIN C OF SH3 PEPTOID INHIBITOR
2AC2SOFTWAREPHE B:263 , GLU B:269 , SER B:270 , GLU B:272 , ASN B:290 , TRP B:291 , ILE B:302 , ASN B:306 , TYR B:307 , HOH D:3 , HOH D:6 , HOH D:20 , HOH D:26 , HOH D:60BINDING SITE FOR CHAIN D OF SH3 PEPTOID INHIBITOR

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:209 -B:309

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2SEM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2SEM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2SEM)

(-) Exons   (0, 0)

(no "Exon" information available for 2SEM)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:58
 aligned with SEM5_CAEEL | P29355 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:58
                                   164       174       184       194       204        
           SEM5_CAEEL   155 ETKFVQALFDFNPQESGELAFKRGDVITLINKDDPNWWEGQLNNRRGIFPSNYVCPYN 212
               SCOP domains d2sema_ A:                                                 SCOP domains
               CATH domains 2semA00 A:155-212 SH3 Domains                              CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..................eeeeee.....eeeeee..eeeeeehhheee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 2sem A 155 ETKFVQALFDFNPQESGELAFKRGDVITLINKDDPNWWEGQLNNRRGIFPSNYVCPYN 212
                                   164       174       184       194       204        

Chain B from PDB  Type:PROTEIN  Length:59
 aligned with SEM5_CAEEL | P29355 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:59
                                   165       175       185       195       205         
           SEM5_CAEEL   156 TKFVQALFDFNPQESGELAFKRGDVITLINKDDPNWWEGQLNNRRGIFPSNYVCPYNSN 214
               SCOP domains d2semb_ B:                                                  SCOP domains
               CATH domains 2semB00 B:256-314 SH3 Domains                               CATH domains
           Pfam domains (1) ----SH3_1-2semB01 B:260-305                       --------- Pfam domains (1)
           Pfam domains (2) ----SH3_1-2semB02 B:260-305                       --------- Pfam domains (2)
         Sec.struct. author ..eeee..................eeeeee.....eeeeee..eeeeeehhheeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 2sem B 256 TKFVQALFDFNPQESGELAFKRGDVITLINKDDPNWWEGQLNNRRGIFPSNYVCPYNSN 314
                                   265       275       285       295       305         

Chain C from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 2sem C   1 xPPPVgPR   8
                            |    |  
                            1-ACE|  
                                 6-IPG

Chain D from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 2sem D  11 xPPPVgPRR  19
                            |    |   
                            |    |   
                           11-ACE|   
                                16-IPG

   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: SH3 (175)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SEM5_CAEEL | P29355)
molecular function
    GO:0005070    SH3/SH2 adaptor activity    Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68).
    GO:0005154    epidermal growth factor receptor binding    Interacting selectively and non-covalently with the epidermal growth factor receptor.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0030539    male genitalia development    The process whose specific outcome is the progression of the male genitalia over time, from its formation to the mature structure.
    GO:0007517    muscle organ development    The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
    GO:0002119    nematode larval development    The process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew.
    GO:0009967    positive regulation of signal transduction    Any process that activates or increases the frequency, rate or extent of signal transduction.
    GO:0031344    regulation of cell projection organization    Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections.
    GO:0040028    regulation of vulval development    Any process that modulates the frequency, rate or extent of development of the vulva. Vulval development is the process whose specific outcome is the progression of the egg-laying organ of female and hermaphrodite nematodes over time, from its formation to the mature structure. In nematodes, the vulva is formed from ventral epidermal cells during larval stages to give rise to a fully formed vulva in the adult.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SEM5_CAEEL | P293551k76 1kfz 1sem 3sem

(-) Related Entries Specified in the PDB File

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