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 2.05 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 2.05: 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 2.05: 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 2.05: 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 2.05: 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 2.05: 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 2.05: 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 2.05: 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 2.05: 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