PDB entry 3dvn

View 3dvn on RCSB PDB site
Description: Crystal structure of K63-specific fab Apu2.16 bound to K63-linked di-ubiquitin
Class: immune system
Keywords: di-ubiquitin, fab fragment, antibody, Nucleus, Phosphoprotein, Ribosomal rotein, IMMUNE SYSTEM
Deposited on 2008-07-18, released 2008-09-30
The last revision prior to the SCOPe 2.03 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-08.
Experiment type: XRAY
Resolution: 2.7 Å
R-factor: 0.223
AEROSPACI score: 0.27 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Human IgG1 fab fragment light chain
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
    Gene: fab fragment light chain
    Database cross-references and differences (RAF-indexed):
    • PDB 3DVG (Start-216)
    Domains in SCOPe 2.03: d3dvna1, d3dvna2
  • Chain 'B':
    Compound: Human IgG1 fab fragment heavy chain
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
    Gene: fab fragment light chain
    Database cross-references and differences (RAF-indexed):
    • PDB 3DVG
    Domains in SCOPe 2.03: d3dvnb1, d3dvnb2
  • Chain 'H':
    Compound: Human IgG1 fab fragment heavy chain
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
    Gene: fab fragment light chain
    Database cross-references and differences (RAF-indexed):
    • PDB 3DVG
    Domains in SCOPe 2.03: d3dvnh1, d3dvnh2
  • Chain 'L':
    Compound: Human IgG1 fab fragment light chain
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
    Gene: fab fragment light chain
    Database cross-references and differences (RAF-indexed):
    • PDB 3DVG (Start-216)
    Domains in SCOPe 2.03: d3dvnl1, d3dvnl2
  • Chain 'U':
    Compound: Ubiquitin D77
    Species: Homo sapiens [TaxId:9606]
    Gene: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62988 (3-End)
      • expression tag (1-2)
    Domains in SCOPe 2.03: d3dvnu_
  • Chain 'V':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62988 (3-78)
      • engineered (65)
    Domains in SCOPe 2.03: d3dvnv_
  • Chain 'X':
    Compound: Ubiquitin D77
    Species: Homo sapiens [TaxId:9606]
    Gene: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62988 (3-End)
      • expression tag (1-2)
    Domains in SCOPe 2.03: d3dvnx_
  • Chain 'Y':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62988 (3-78)
      • engineered (65)
    Domains in SCOPe 2.03: d3dvny_

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3dvnA (A:)
    sdiqmtqspsslsasvgdrvtitcrasqsvssavawyqqkpgkapklliysasslysgvp
    srfsgsrsgtdftltisslqpedfatyycqqyssysslftfgqgtkveikrtvaapsvfi
    fppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslss
    tltlskadyekhkvyacevthqglsspvtksfnrgec
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dvnA (A:)
    tqspsslsasvgdrvtitcrasqsvssavawyqqkpgkapklliysasslysgvpsrfsg
    srsgtdftltisslqpedfatyycqqyssysslftfgqgtkveikrtvaapsvfifppsd
    eqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstltls
    kadyekhkvyacevthqglsspvtksfnrgec
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3dvnB (B:)
    eisevqlvesggglvqpggslrlscaasgfnvktglihwvrqapgkglewvayispyygs
    tsyadsvkgrftisadtskntaylqmnslraedtavyycareyyrwytaidywgqgtlvt
    vssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavl
    qssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscdkth
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dvnB (B:)
    evqlvesggglvqpggslrlscaasgfnvktglihwvrqapgkglewvayispyygstsy
    adsvkgrftisadtskntaylqmnslraedtavyycareyyrwytaidywgqgtlvtvss
    astkgpsvfplapssggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglys
    lssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >3dvnH (H:)
    eisevqlvesggglvqpggslrlscaasgfnvktglihwvrqapgkglewvayispyygs
    tsyadsvkgrftisadtskntaylqmnslraedtavyycareyyrwytaidywgqgtlvt
    vssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavl
    qssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscdkth
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dvnH (H:)
    evqlvesggglvqpggslrlscaasgfnvktglihwvrqapgkglewvayispyygstsy
    adsvkgrftisadtskntaylqmnslraedtavyycareyyrwytaidywgqgtlvtvss
    astkgpsvfplapssggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglys
    lssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >3dvnL (L:)
    sdiqmtqspsslsasvgdrvtitcrasqsvssavawyqqkpgkapklliysasslysgvp
    srfsgsrsgtdftltisslqpedfatyycqqyssysslftfgqgtkveikrtvaapsvfi
    fppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslss
    tltlskadyekhkvyacevthqglsspvtksfnrgec
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dvnL (L:)
    tqspsslsasvgdrvtitcrasqsvssavawyqqkpgkapklliysasslysgvpsrfsg
    srsgtdftltisslqpedfatyycqqyssysslftfgqgtkveikrtvaapsvfifppsd
    eqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstltls
    kadyekhkvyacevthqglsspvtksfnrgec
    

  • Chain 'U':
    Sequence, based on SEQRES records: (download)
    >3dvnU (U:)
    gshmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtls
    dyniqkestlhlvlrlrggd
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dvnU (U:)
    shmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsd
    yniqkestlhlvlrl
    

  • Chain 'V':
    Sequence, based on SEQRES records: (download)
    >3dvnV (V:)
    gshmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtls
    dyniqrestlhlvlrlrgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dvnV (V:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqrestlhlvlrlrgg
    

  • Chain 'X':
    Sequence, based on SEQRES records: (download)
    >3dvnX (X:)
    gshmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtls
    dyniqkestlhlvlrlrggd
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dvnX (X:)
    shmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsd
    yniqkestlhlvlrl
    

  • Chain 'Y':
    Sequence, based on SEQRES records: (download)
    >3dvnY (Y:)
    gshmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtls
    dyniqrestlhlvlrlrgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dvnY (Y:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqrestlhlvlrlrgg