PDB entry 2vi6

View 2vi6 on RCSB PDB site
Description: crystal structure of the nanog homeodomain
Class: transcription
Keywords: homeodomain, DNA-binding, transcription, transcription factor, developmental protein, transcription regulation, nanog, nucleus, homeobox, activator, repressor
Deposited on 2007-11-28, released 2008-01-15
The last revision prior to the SCOPe 2.07 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-31.
Experiment type: XRAY
Resolution: 2.6 Å
R-factor: 0.223
AEROSPACI score: 0.28 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: homeobox protein nanog
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 2VI6
    • Uniprot Q80Z64 (Start-61)
    Domains in SCOPe 2.07: d2vi6a_
  • Chain 'B':
    Compound: homeobox protein nanog
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 2VI6
    • Uniprot Q80Z64 (Start-61)
    Domains in SCOPe 2.07: d2vi6b_
  • Chain 'C':
    Compound: homeobox protein nanog
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 2VI6
    • Uniprot Q80Z64 (Start-61)
    Domains in SCOPe 2.07: d2vi6c_
  • Chain 'D':
    Compound: homeobox protein nanog
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 2VI6
    • Uniprot Q80Z64 (Start-61)
    Domains in SCOPe 2.07: d2vi6d_
  • Chain 'E':
    Compound: homeobox protein nanog
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 2VI6
    • Uniprot Q80Z64 (Start-61)
    Domains in SCOPe 2.07: d2vi6e_
  • Chain 'F':
    Compound: homeobox protein nanog
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 2VI6
    • Uniprot Q80Z64 (Start-61)
    Domains in SCOPe 2.07: d2vi6f_
  • Chain 'G':
    Compound: homeobox protein nanog
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 2VI6
    • Uniprot Q80Z64 (Start-61)
    Domains in SCOPe 2.07: d2vi6g_
  • Chain 'H':
    Compound: homeobox protein nanog
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 2VI6
    • Uniprot Q80Z64 (Start-61)
    Domains in SCOPe 2.07: d2vi6h_
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >2vi6A (A:)
gtkqkmrtvfsqaqlcalkdrfqkqkylslqqmqelssilnlsykqvktwfqnqrmkckr
wq

    Sequence, based on observed residues (ATOM records): (download) 
    >2vi6A (A:)
tvfsqaqlcalkdrfqkqkylslqqmqelssilnlsykqvktwfqnqrmkckrwq

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >2vi6B (B:)
gtkqkmrtvfsqaqlcalkdrfqkqkylslqqmqelssilnlsykqvktwfqnqrmkckr
wq

    Sequence, based on observed residues (ATOM records): (download) 
    >2vi6B (B:)
vfsqaqlcalkdrfqkqkylslqqmqelssilnlsykqvktwfqnqrmkckrwq

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >2vi6C (C:)
gtkqkmrtvfsqaqlcalkdrfqkqkylslqqmqelssilnlsykqvktwfqnqrmkckr
wq

    Sequence, based on observed residues (ATOM records): (download) 
    >2vi6C (C:)
tvfsqaqlcalkdrfqkqkylslqqmqelssilnlsykqvktwfqnqrmkckrwq

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >2vi6D (D:)
gtkqkmrtvfsqaqlcalkdrfqkqkylslqqmqelssilnlsykqvktwfqnqrmkckr
wq

    Sequence, based on observed residues (ATOM records): (download) 
    >2vi6D (D:)
tvfsqaqlcalkdrfqkqkylslqqmqelssilnlsykqvktwfqnqrmkckrwq

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >2vi6E (E:)
gtkqkmrtvfsqaqlcalkdrfqkqkylslqqmqelssilnlsykqvktwfqnqrmkckr
wq

    Sequence, based on observed residues (ATOM records): (download) 
    >2vi6E (E:)
vfsqaqlcalkdrfqkqkylslqqmqelssilnlsykqvktwfqnqrmkckrwq

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >2vi6F (F:)
gtkqkmrtvfsqaqlcalkdrfqkqkylslqqmqelssilnlsykqvktwfqnqrmkckr
wq

    Sequence, based on observed residues (ATOM records): (download) 
    >2vi6F (F:)
tvfsqaqlcalkdrfqkqkylslqqmqelssilnlsykqvktwfqnqrmkckrwq

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >2vi6G (G:)
gtkqkmrtvfsqaqlcalkdrfqkqkylslqqmqelssilnlsykqvktwfqnqrmkckr
wq

    Sequence, based on observed residues (ATOM records): (download) 
    >2vi6G (G:)
tvfsqaqlcalkdrfqkqkylslqqmqelssilnlsykqvktwfqnqrmkckrwq

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >2vi6H (H:)
gtkqkmrtvfsqaqlcalkdrfqkqkylslqqmqelssilnlsykqvktwfqnqrmkckr
wq

    Sequence, based on observed residues (ATOM records): (download) 
    >2vi6H (H:)
vfsqaqlcalkdrfqkqkylslqqmqelssilnlsykqvktwfqnqrmkckrwq