PDB entry 1ybo

View 1ybo on RCSB PDB site
Description: Crystal structure of the PDZ tandem of human syntenin with syndecan peptide
Class: structural protein
Keywords: PDZ domain, scaffolding protein, adhesion complex
Deposited on 2004-12-21, released 2006-01-10
The last revision prior to the SCOP 1.73 freeze date was dated 2006-11-07, with a file datestamp of 2007-06-28.
Experiment type: XRAY
Resolution: 2.3 Å
R-factor: 0.193
AEROSPACI score: 0.39 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Syntenin 1
    Species: HOMO SAPIENS
    Gene: SDCBP, MDA9, SYCL
    Database cross-references and differences (RAF-indexed):
    • Uniprot O00560 (5-165)
      • cloning artifact (3-4)
    Domains in SCOP 1.73: d1yboa1, d1yboa2
  • Chain 'B':
    Compound: Syntenin 1
    Species: HOMO SAPIENS
    Gene: SDCBP, MDA9, SYCL
    Database cross-references and differences (RAF-indexed):
    • Uniprot O00560 (5-End)
      • cloning artifact (1-4)
    Domains in SCOP 1.73: d1ybob1, d1ybob2
  • Chain 'C':
    Compound: syndecan-4
    Species: synthetic, synthetic
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: syndecan-4
    Species: synthetic, synthetic
    Database cross-references and differences (RAF-indexed):
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >1yboA (A:)
gamdprevilckdqdgkiglrlksidngifvqlvqanspaslvglrfgdqvlqingenca
gwssdkahkvlkqafgekitmtirdrpfertitmhkdstghvgfifkngkitsivkdssa
arnglltehniceingqnviglkdsqiadilstsgtvvtitimpaf

    Sequence, based on observed residues (ATOM records): (download) 
    >1yboA (A:)
dprevilckdqdgkiglrlksidngifvqlvqanspaslvglrfgdqvlqingencagws
sdkahkvlkqafgekitmtirdrpfertitmhkdstghvgfifkngkitsivkdssaarn
glltehniceingqnviglkdsqiadilstsgtvvtitimpaf

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >1yboB (B:)
gamdprevilckdqdgkiglrlksidngifvqlvqanspaslvglrfgdqvlqingenca
gwssdkahkvlkqafgekitmtirdrpfertitmhkdstghvgfifkngkitsivkdssa
arnglltehniceingqnviglkdsqiadilstsgtvvtitimpaf

    Sequence, based on observed residues (ATOM records): (download) 
    >1yboB (B:)
amdprevilckdqdgkiglrlksidngifvqlvqanspaslvglrfgdqvlqingencag
wssdkahkvlkqafgekitmtirdrpfertitmhkdstghvgfifkngkitsivkdssaa
rnglltehniceingqnviglkdsqiadilstsgtvvtitimpa

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    No sequence available.