Lineage for Family b.1.1.1: V set domains (antibody variable domain-like)

  1. Root: SCOPe 2.06
  2. 2017114Class b: All beta proteins [48724] (177 folds)
  3. 2017115Fold b.1: Immunoglobulin-like beta-sandwich [48725] (33 superfamilies)
    sandwich; 7 strands in 2 sheets; greek-key
    some members of the fold have additional strands
  4. 2017116Superfamily b.1.1: Immunoglobulin [48726] (5 families) (S)
  5. 2017117Family b.1.1.1: V set domains (antibody variable domain-like) [48727] (33 protein domains)

Protein Domains:

  1. 2017118Alphaherpesvirus glycoprotein E [141008] (1 species)
    elaborated with insertions and C-terminal extensions
  2. 2017124B- and T-lymphocyte attenuator CD272 [158869] (1 species)
  3. 2017128Biliary glycoprotein C (CD66a, CEACAM1A[1,4]), N-terminal domain [81942] (1 species)
  4. 2017131Camelid IG heavy chain variable domain, VHh [88563] (3 species)
    1. 2017132Species Camel (Camelus dromedarius) [TaxId:9838] [88564] (19 PDB entries)
      SQ NA # camelid antibody
    2. 2017166Species Human (Homo sapiens) [TaxId:9606] [158863] (2 PDB entries)
    3. 2017171Species Llama (Lama glama) [TaxId:9844] [88565] (7 PDB entries)
  5. 2017180CD2, first domain [48740] (2 species)
    1. 2017181Species Human (Homo sapiens) [TaxId:9606] [48741] (4 PDB entries)
    2. 2017187Species Norway rat (Rattus norvegicus) [TaxId:10116] [48742] (5 PDB entries)
  6. 2017200CD2-binding domain of CD58, N-terminal domain [48743] (1 species)
  7. 2017206CD28 [158865] (1 species)
    T-cell-specific surface glycoprotein
  8. 2017209CD4 V-set domains [48737] (2 species)
    1. 2017210Species Human (Homo sapiens) [TaxId:9606] [48738] (32 PDB entries)
    2. 2017254Species Rat (Rattus rattus) [TaxId:10117] [48739] (1 PDB entry)
  9. 2017256CD8 [48734] (3 species)
    1. 2017257Species Human (Homo sapiens) [TaxId:9606] [48735] (3 PDB entries)
    2. 2017265Species Mouse (Mus musculus) [TaxId:10090] [48736] (5 PDB entries)
    3. 2017278Species Mouse (Mus musculus), beta-chain [TaxId:10090] [158864] (2 PDB entries)
      Uniprot P10300 22-136
  10. 2017283CD80, N-terminal domain [48745] (1 species)
    a soluble form of b7-1
  11. 2017288CD86 (b7-2), N-terminal domain [63635] (1 species)
  12. 2017294Coxsackie virus and adenovirus receptor (Car), domain 1 [48730] (1 species)
  13. 2017316HSV glycoprotein D [63637] (1 species)
  14. 2017323Immunoglobulin heavy chain variable domain, VH [88543] (21 species)
    VH domains of human and mouse antibodies are clustered by the sequence similarity within the germline encoded segment and then by the size of the complementarity determining regions CDR1 and CDR2, so the clusters may correspond to putative germline families in the species genomes; VH domains with artificial or grafted exogenous CDRs are listed as engineered species
    1. 2017324Species Chinese hamster (Cricetulus griseus) [TaxId:10029] [88561] (1 PDB entry)
    2. 2017327Species Engineered (including hybrid species) [88562] (68 PDB entries)
      SQ NA # humanized antidoby; bactericidal Fab-h6831 ! SQ NA # humanized antibody ! SQ NA # Humanized antibody ! SQ NA # engineered antibody
    3. 2017430Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88544] (37 PDB entries)
    4. 2017491Species Human (Homo sapiens), cluster 2.1 [TaxId:9606] [88545] (3 PDB entries)
    5. 2017497Species Human (Homo sapiens), cluster 2.2 [TaxId:9606] [88546] (2 PDB entries)
    6. 2017500Species Human (Homo sapiens), cluster 3 [TaxId:9606] [88547] (33 PDB entries)
      Uniprot Q6N089 20-243 # 95% sequence identity; natural chimera: antibody heavy chain (Fab HYB3)
    7. 2017572Species Human (Homo sapiens), cluster 4 [TaxId:9606] [101505] (4 PDB entries)
    8. 2017580Species Mouse (Mus musculus), cluster 1 [TaxId:10090] [88548] (68 PDB entries)
      Uniprot P01796 # ! HV27_MOUSE Ig heavy chain V-III region A4
    9. 2017670Species Mouse (Mus musculus), cluster 2.1 [TaxId:10090] [88549] (15 PDB entries)
      Uniprot P18527 # HV56_MOUSE Ig heavy chain V region 914; 90% sequence identity
    10. 2017693Species Mouse (Mus musculus), cluster 2.2 [TaxId:10090] [88550] (59 PDB entries)
      Uniprot P01811 # HV41_MOUSE (P01811) Ig heavy chain V region UPC10
    11. 2017783Species Mouse (Mus musculus), cluster 3.1 [TaxId:10090] [88551] (31 PDB entries)
      SQ NA # natural chimera; best hits are: Uniprot P01751 (Ig heavy chain V region B1-8/186-2) and Uniprot P01864 (Ig gamma-2A chain C region secreted form)
    12. 2017824Species Mouse (Mus musculus), cluster 3.2 [TaxId:10090] [88552] (181 PDB entries)
      Uniprot P01756 1-117 # 78% sequense identity; HV12_MOUSE Ig heavy chain V region MOPC 104E ! SQ NA # humanized antibody ! Uniprot P01750 # HV06_MOUSE Ig heavy chain V region 102 precursor ! Uniprot P01750 20-116 # ! HV06_MOUSE Ig heavy chain V region 102 precursor
    13. 2018052Species Mouse (Mus musculus), cluster 3.3 [TaxId:10090] [88553] (1 PDB entry)
    14. 2018055Species Mouse (Mus musculus), cluster 4 [TaxId:10090] [88554] (34 PDB entries)
      Uniprot P06327 20-117 # HV52_MOUSE (P06327) Ig heavy chain V region VH558 A1/A4 precursor; 57% sequence identity ! Uniprot P01631 # KV2G_MOUSE (P01631) Ig kappa chain V-II region 26-10
    15. 2018105Species Mouse (Mus musculus), cluster 5 [TaxId:10090] [88555] (36 PDB entries)
    16. 2018153Species Mouse (Mus musculus), cluster 6 [TaxId:10090] [88556] (12 PDB entries)
      SQ NA # part of Fab 28 against HIV-1 RT
    17. 2018168Species Mouse (Mus musculus), cluster 7.1 [TaxId:10090] [88557] (39 PDB entries)
      Uniprot P18532 # HV61_MOUSE Ig heavy chain V region 1B43 precursor
    18. 2018217Species Mouse (Mus musculus), cluster 7.2 [TaxId:10090] [88558] (32 PDB entries)
    19. 2018252Species Mouse (Mus musculus), cluster 7.3 [TaxId:10090] [88559] (2 PDB entries)
    20. 2018255Species Norway rat (Rattus norvegicus) [TaxId:10116] [88560] (16 PDB entries)
    21. 2018288Species Synthetic construct [TaxId:32630] [158862] (3 PDB entries)
  15. 2018294Immunoglobulin light chain kappa variable domain, VL-kappa [88519] (16 species)
    VL-kappa domains of human and mouse antibodies are clustered by the sequence similarity within the germline encoded segment and then by the size of the complementarity determining regions CDR1 and CDR2, so the clusters may correspond to putative germline families in the species genomes; VL-kappa domains with artificial or grafted exogenous CDRs are listed as engineered species
    1. 2018295Species Engineered (including hybrid species) [88533] (61 PDB entries)
      SQ NA # humanized antidoby; bactericidal Fab-h6831 ! SQ NA # Humanized antibody ! SQ NA # humanized antibody ! SQ NA # engineered antibody
    2. 2018377Species Escherichia coli [TaxId:562] [224853] (1 PDB entry)
    3. 2018379Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88520] (19 PDB entries)
    4. 2018423Species Human (Homo sapiens), cluster 2 [TaxId:9606] [88521] (10 PDB entries)
    5. 2018439Species Human (Homo sapiens), cluster 3.1 [TaxId:9606] [88522] (8 PDB entries)
    6. 2018454Species Human (Homo sapiens), cluster 3.2 [TaxId:9606] [88523] (31 PDB entries)
    7. 2018517Species Mouse (Mus musculus), cluster 1.1 [TaxId:10090] [88524] (132 PDB entries)
      Uniprot P01631 #KV2G_MOUSE Ig kappa chain V-II region 26-10; 79% sequence identity ! Uniprot P06310 # KV2F_HUMAN IG KAPPA CHAIN V-II REGION RPMI 6410 PRECURSOR ! Uniprot P03976 # KV2E_MOUSE (P03976) Ig kappa chain V-II region 17S29.1 ! Uniprot P01642 21-115 # ! KV2G_MOUSE IG KAPPA CHAIN V-II REGION 26-10
    8. 2018687Species Mouse (Mus musculus), cluster 1.2 [TaxId:10090] [88525] (51 PDB entries)
    9. 2018756Species Mouse (Mus musculus), cluster 2 [TaxId:10090] [88526] (28 PDB entries)
    10. 2018797Species Mouse (Mus musculus), cluster 3.1 [TaxId:10090] [88527] (13 PDB entries)
    11. 2018816Species Mouse (Mus musculus), cluster 3.2 [TaxId:10090] [88528] (40 PDB entries)
      Uniprot P04940 # KV6F_MOUSE IG KAPPA CHAIN V-VI REGION NQ2-17.4.1
    12. 2018884Species Mouse (Mus musculus), cluster 3.3 [TaxId:10090] [88529] (2 PDB entries)
    13. 2018888Species Mouse (Mus musculus), cluster 3.4 [TaxId:10090] [88530] (4 PDB entries)
    14. 2018893Species Mouse (Mus musculus), cluster 4 [TaxId:10090] [88531] (217 PDB entries)
      Uniprot P01645 1-106 # 95% sequense identity; KV5L_MOUSE Ig kappa chain V-V region HP 93G7 ! SQ NA # natural chimera; best hits are: Uniprot P01637 (Ig kappa chain V-V region T1) and Uniprot P01837 (Ig kappa chain C region) ! SQ NA # humanized antibody ! SQ NA # part of Fab 28 against HIV-1 RT ! Uniprot P01642 21-115 # ! KV5I_MOUSE Ig kappa chain V-V region L7 precursor
    15. 2019161Species Norway rat (Rattus norvegicus) [TaxId:10116] [88532] (9 PDB entries)
    16. 2019179Species Synthetic construct [TaxId:32630] [158859] (2 PDB entries)
  16. 2019185Immunoglobulin light chain lambda variable domain, VL-lambda [88534] (9 species)
    VL-lambda domains of human antibodies are clustered by the sequence similarity within the germline encoded segment and then by the size of the complementarity determining regions CDR1 and CDR2, so the clusters may correspond to putative germline families in the human genome; mouse VL-lambda domains belong to a single germline family
    1. 2019186Species Chinese hamster (Cricetulus griseus) [TaxId:10029] [88542] (1 PDB entry)
    2. 2019189Species Human (Homo sapiens), cluster 1 [TaxId:9606] [88535] (4 PDB entries)
      SQ NA # Bence-Jones protein JTO ! Uniprot P06317 # Ig lambda chain V-VI region SUT
    3. 2019198Species Human (Homo sapiens), cluster 2 [TaxId:9606] [88536] (10 PDB entries)
    4. 2019213Species Human (Homo sapiens), cluster 3.1 [TaxId:9606] [88537] (1 PDB entry)
    5. 2019215Species Human (Homo sapiens), cluster 3.2 [TaxId:9606] [88538] (1 PDB entry)
    6. 2019217Species Human (Homo sapiens), cluster 4 [TaxId:9606] [88539] (23 PDB entries)
    7. 2019263Species Human (Homo sapiens), cluster 5 [TaxId:9606] [88540] (7 PDB entries)
      Uniprot Q8N355 20-230 # 94% sequence identity; natural chimera: antibody light chain (Fab HYB3)
    8. 2019276Species Mouse (Mus musculus) [TaxId:10090] [88541] (35 PDB entries)
    9. 2019324Species Norway rat (Rattus norvegicus) [TaxId:10116] [101504] (7 PDB entries)
  17. 2019345Immunoreceptor CTLA-4 (CD152), N-terminal fragment [48939] (2 species)
    1. 2019346Species Human (Homo sapiens) [TaxId:9606] [48940] (4 PDB entries)
    2. 2019353Species Mouse (Mus musculus) [TaxId:10090] [48941] (3 PDB entries)
  18. 2019359Junction adhesion molecule, JAM, N-terminal domain [48747] (2 species)
    1. 2019360Species Human (Homo sapiens) [TaxId:9606] [89180] (1 PDB entry)
    2. 2019363Species Mouse (Mus musculus) [TaxId:10090] [48748] (1 PDB entry)
  19. 2019365Kin of IRRE-like protein 3, KIRREL3 [158867] (1 species)
  20. 2019368Myelin membrane adhesion molecule P0 [48728] (1 species)
  21. 2019371Myelin oligodendrocyte glycoprotein (MOG) [89174] (1 species)
  22. 2019378N-terminal domain of sialic acid binding Ig-like lectin 7 (SIGLEC-7, p75/AIRM1) [89176] (1 species)
  23. 2019386N-terminal domain of sialoadhesin [48732] (1 species)
  24. 2019396NK cell activating receptor NKP44 [89178] (1 species)
    a triggering partner in natural cytotoxicity
  25. 2019399Novel antigen receptor (against lysozyme) [110042] (1 species)
  26. 2019405Novel antigen receptor 12Y-1 [110044] (1 species)
  27. 2019408Novel antigen receptor 12Y-2 [110046] (1 species)
  28. 2019412Polymeric-immunoglobulin receptor, PIGR [117038] (1 species)
  29. 2019420Programmed cell death protein 1, PD1, extracellular domain [101510] (2 species)
    1. 2019421Species Human (Homo sapiens) [TaxId:9606] [256383] (3 PDB entries)
    2. 2019424Species Mouse (Mus musculus) [TaxId:10090] [101511] (6 PDB entries)
  30. 2019432T-cell antigen receptor [48933] (6 species)
    sequences may differ within each classified species
    1. 2019433Species Human (Homo sapiens), alpha-chain [TaxId:9606] [48935] (21 PDB entries)
    2. 2019460Species Human (Homo sapiens), beta-chain [TaxId:9606] [48937] (29 PDB entries)
    3. 2019513Species Human (Homo sapiens), delta-chain [TaxId:9606] [48938] (3 PDB entries)
    4. 2019522Species Human (Homo sapiens), gamma-chain [TaxId:9606] [63651] (3 PDB entries)
    5. 2019537Species Mouse (Mus musculus), alpha-chain [TaxId:10090] [48934] (22 PDB entries)
    6. 2019575Species Mouse (Mus musculus), beta-chain [TaxId:10090] [48936] (28 PDB entries)
  31. 2019619TREM-1 (triggering receptor expressed on myeloid cells 1) [101506] (2 species)
    1. 2019620Species Human (Homo sapiens) [TaxId:9606] [101507] (2 PDB entries)
      Uniprot Q9NP99 21-133
    2. 2019627Species Mouse (Mus musculus) [TaxId:10090] [117037] (1 PDB entry)
      Uniprot Q9JKE2 25-134
  32. 2019630Tyrosine-protein kinase receptor tyro3, N-terminal domain [101508] (1 species)
  33. 2019634automated matches [190119] (22 species)
    not a true protein
    1. 2019635Species Camel (Camelus dromedarius) [TaxId:9838] [187219] (31 PDB entries)
    2. 2019688Species Cow (Bos taurus) [TaxId:9913] [197337] (2 PDB entries)
    3. 2019690Species Dogfish (Squalus acanthias) [TaxId:7797] [226656] (2 PDB entries)
    4. 2019694Species Human (Homo sapiens) [TaxId:9606] [188740] (171 PDB entries)
    5. 2019995Species Human herpesvirus 1 [TaxId:10299] [256116] (1 PDB entry)
    6. 2019997Species Human herpesvirus 2 [TaxId:10313] [259821] (1 PDB entry)
    7. 2020000Species Human herpesvirus 2 [TaxId:10315] [256151] (1 PDB entry)
    8. 2020002Species Lepus curpaeums [TaxId:9980] [279011] (1 PDB entry)
    9. 2020007Species Llama (Lama glama) [TaxId:9844] [187485] (134 PDB entries)
    10. 2020193Species Llama glama [TaxId:9844] [236993] (1 PDB entry)
    11. 2020200Species Macaca mulatta [TaxId:9541] [188468] (1 PDB entry)
    12. 2020203Species Mouse (Mus musculus) [TaxId:10090] [186842] (156 PDB entries)
    13. 2020466Species Norway rat (Rattus norvegicus) [TaxId:10116] [187415] (7 PDB entries)
    14. 2020482Species Nurse shark (Ginglymostoma cirratum) [TaxId:7801] [187220] (4 PDB entries)
    15. 2020490Species Ornithorhynchus anatinus [TaxId:9258] [228732] (1 PDB entry)
    16. 2020492Species Rat (Rattus rattus) [TaxId:10117] [225551] (1 PDB entry)
    17. 2020495Species Spotted wobbegong (Orectolobus maculatus) [TaxId:168098] [187564] (8 PDB entries)
    18. 2020506Species Vicugna pacos [TaxId:30538] [189756] (28 PDB entries)
    19. 2270864Species Helicobacter pylori [TaxId:210] [314169] (1 PDB entry)
    20. 2279247Species Sus scrofa [TaxId:9823] [322548] (1 PDB entry)
    21. 2288171Species Oryctolagus cuniculus [TaxId:9986] [331472] (1 PDB entry)
    22. 2292807Species Escherichia coli [TaxId:562] [336108] (1 PDB entry)

More info for Family b.1.1.1: V set domains (antibody variable domain-like)

Timeline for Family b.1.1.1: V set domains (antibody variable domain-like):