Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) 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. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Sh3 Domain, Inhibitors, Peptoids, Protein-Protein Recognition, Proline-Rich Motifs, Signal Transduction, 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 - SEX MUSCLE ABNORMAL PROTEIN 5
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: C-TERMINAL SH3
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
 
Molecule 2 - SH3 PEPTOID INHIBITOR
    Chains: C, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NMC2Mod. Amino AcidN-CYCLOPROPYLMETHYL GLYCINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NMC1Mod. Amino AcidN-CYCLOPROPYLMETHYL GLYCINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NMC1Mod. Amino AcidN-CYCLOPROPYLMETHYL GLYCINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:163 , GLN A:168 , GLU A:169 , GLU A:172 , ASN A:190 , TRP A:191 , PRO A:204 , ASN A:206 , TYR A:207BINDING SITE FOR CHAIN C OF SH3 PEPTOID INHIBITOR
2AC2SOFTWAREPHE B:263 , ASN B:290 , TRP B:291 , PRO B:304 , ASN B:306 , TYR B:307BINDING SITE FOR CHAIN D OF SH3 PEPTOID INHIBITOR

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SEM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SEM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SEM)

(-) Exons   (0, 0)

(no "Exon" information available for 3SEM)

(-) Sequences/Alignments

Asymmetric 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 d3sema_ A:                                                 SCOP domains
               CATH domains 3semA00 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
                 3sem A 155 ETKFVQALFDFNPQESGELAFKRGDVITLINKDDPNWWEGQLNNRRGIFPSNYVCPYN 212
                                   164       174       184       194       204        


Chain B 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 d3semb_ B:                                                 SCOP domains
               CATH domains 3semB00 B:255-312 SH3 Domains                              CATH domains
           Pfam domains (1) -----SH3_1-3semB01 B:260-305                       ------- Pfam domains (1)
           Pfam domains (2) -----SH3_1-3semB02 B:260-305                       ------- Pfam domains (2)
         Sec.struct. author ...eeee..................eeeeee.....eeeeee..eeeeeehhheee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 3sem B 255 ETKFVQALFDFNPQESGELAFKRGDVITLINKDDPNWWEGQLNNRRGIFPSNYVCPYN 312
                                   264       274       284       294       304        


Chain C from PDB  Type:PROTEIN  Length:7
                                       
               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
                 3sem C   2 PPPVgPR   8
                                |  
                                6-NMC


Chain D from PDB  Type:PROTEIN  Length:6
                                      
               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
                 3sem D  12 PPPVgP  17
                                | 
                               16-NMC
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: SH3 (175)

(-) Gene Ontology  (10, 10)

Asymmetric 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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NMC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3sem)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3sem
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SEM5_CAEEL | P29355
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SEM5_CAEEL | P29355
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SEM5_CAEEL | P29355: 1k76 1kfz 1sem 2sem

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3SEM)