PDB entry 4gdk

View 4gdk on RCSB PDB site
Description: Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1
Class: protein binding
Keywords: protein-protein conjugate, protein-protein complex, ubiquitin-like protein, autophagy, E3 ligase, ubiquitin-like fold, structural protein, isopeptide bond, Cytoplasm and autophagosomal membranes, PROTEIN BINDING
Deposited on 2012-07-31, released 2012-12-05
The last revision prior to the SCOPe 2.08 freeze date was dated 2017-11-15, with a file datestamp of 2017-11-10.
Experiment type: XRAY
Resolution: 2.7 Å
R-factor: N/A
AEROSPACI score: 0.19 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Ubiquitin-like protein ATG12
    Species: Homo sapiens [TaxId:9606]
    Gene: APG12, APG12L, ATG12
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4gdka_
  • Chain 'B':
    Compound: Autophagy protein 5
    Species: Homo sapiens [TaxId:9606]
    Gene: APG5L, ASP, ATG5
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: Autophagy-related protein 16-1
    Species: Homo sapiens [TaxId:9606]
    Gene: APG16L, ATG16L1, UNQ9393/PRO34307
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q676U5 (3-35)
      • expression tag (2)
  • Chain 'D':
    Compound: Ubiquitin-like protein ATG12
    Species: Homo sapiens [TaxId:9606]
    Gene: APG12, APG12L, ATG12
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4gdkd_
  • Chain 'E':
    Compound: Autophagy protein 5
    Species: Homo sapiens [TaxId:9606]
    Gene: APG5L, ASP, ATG5
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: Autophagy-related protein 16-1
    Species: Homo sapiens [TaxId:9606]
    Gene: APG16L, ATG16L1, UNQ9393/PRO34307
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q676U5 (3-35)
      • expression tag (1-2)
  • Heterogens: NA, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >4gdkA (A:)
gskkkidillkavgdtpimktkkwavertrtiqglidfikkflklvaseqlfiyvnqsfa
pspdqevgtlyecfgsdgklvlhycksqawg

    Sequence, based on observed residues (ATOM records): (download) 
    >4gdkA (A:)
kkidillkavgdtpimktkkwavertrtiqglidfikkflklvaseqlfiyvnqsfapsp
dqevgtlyecfgsdgklvlhycksqawg

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >4gdkD (D:)
gskkkidillkavgdtpimktkkwavertrtiqglidfikkflklvaseqlfiyvnqsfa
pspdqevgtlyecfgsdgklvlhycksqawg

    Sequence, based on observed residues (ATOM records): (download) 
    >4gdkD (D:)
kidillkavgdtpimktkkwavertrtiqglidfikkflklvaseqlfiyvnqsfapspd
qevgtlyecfgsdgklvlhycksqawg

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    No sequence available.