PDB entry 3dvg
View 3dvg on RCSB PDB site
Description: Crystal structure of K63-specific fab Apu.3A8 bound to K63-linked di-ubiquitin
Class: immune system
Keywords: di-ubiquitin, fab fragment, antibody, Nucleus, Phosphoprotein, Ribosomal protein, IMMUNE SYSTEM
Deposited on
2008-07-18, released
2008-09-30
The last revision prior to the SCOPe 2.01 freeze date was dated
2011-07-13, with a file datestamp of
2011-05-08.
Experiment type: XRAY
Resolution: 2.6 Å
R-factor: 0.224
AEROSPACI score: 0.28
(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):
Domains in SCOPe 2.01: d3dvga1, d3dvga2 - 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):
Domains in SCOPe 2.01: d3dvgb1, d3dvgb2 - 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):
Domains in SCOPe 2.01: d3dvgx_ - Chain 'Y':
Compound: Ubiquitin
Species: Homo sapiens [TaxId:9606]
Gene: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.01: d3dvgy_ - Heterogens: HOH
PDB Chain Sequences:
- Chain 'A':
Sequence, based on SEQRES records: (download)
>3dvgA (A:)
sdiqmtqspsslsasvgdrvtitcrasqsvssavawyqqkpgkapklliysarslysgvp
srfsgsrsgtdftltisslqpedfatyycqqyssysslftfgqgtkveikrtvaapsvfi
fppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslss
tltlskadyekhkvyacevthqglsspvtksfnrgec
Sequence, based on observed residues (ATOM records): (download)
>3dvgA (A:)
tqspsslsasvgdrvtitcrasqsvssavawyqqkpgkapklliysarslysgvpsrfsg
srsgtdftltisslqpedfatyycqqyssysslftfgqgtkveikrtvaapsvfifppsd
eqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstltls
kadyekhkvyacevthqglsspvtksfnrg
- Chain 'B':
Sequence, based on SEQRES records: (download)
>3dvgB (B:)
eisevqlvesggglvqpggslrlscaasgfnvktglihwvrqapgkglewvayitpyygs
tsyadsvkgrftisadtskntaylqmnslraedtavyycareyyrwytaidywgqgtlvt
vssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavl
qssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscdkth
Sequence, based on observed residues (ATOM records): (download)
>3dvgB (B:)
evqlvesggglvqpggslrlscaasgfnvktglihwvrqapgkglewvayitpyygstsy
adsvkgrftisadtskntaylqmnslraedtavyycareyyrwytaidywgqgtlvtvss
astkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqss
glyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk
- Chain 'X':
Sequence, based on SEQRES records: (download)
>3dvgX (X:)
gshmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtls
dyniqkestlhlvlrlrggd
Sequence, based on observed residues (ATOM records): (download)
>3dvgX (X:)
shmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsd
yniqkestlhlvlrl
- Chain 'Y':
Sequence, based on SEQRES records: (download)
>3dvgY (Y:)
gshmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtls
dyniqrestlhlvlrlrgg
Sequence, based on observed residues (ATOM records): (download)
>3dvgY (Y:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqrestlhlvlrlrgg