Structural Classification of Proteins
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Superfamily: Homeodomain-like

consists only of helices
link to SUPERFAMILY database - Superfamily

Lineage:

  1. Root: scop
  2. Class: All alpha proteins [46456]
  3. Fold: DNA/RNA-binding 3-helical bundle [46688]
    core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down
  4. Superfamily: Homeodomain-like [46689]
    consists only of helices
    link to SUPERFAMILY database - Superfamily

Families:

  1. Homeodomain [46690] (42)
    Pfam 00046
    1. Engrailed Homeodomain [46691]
      1. Drosophila melanogaster [TaxId: 7227] [46692] (10) picpic
    2. Mating type protein A1 Homeodomain [46693]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [46694] (6) picpic
    3. mat alpha2 Homeodomain [46695]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [46696] (6) picpic
    4. Hepatocyte nuclear factor 1a (LFB1/HNF1) [46697]
      atypical Homeodomain with a large insertion into HTH motif
      1. Rat (Rattus rattus) [TaxId: 10117] [46698] (2) picpic
      2. Human (Homo sapiens) [TaxId: 9606] [81680] (1) picpic
    5. Oct-1 POU Homeodomain [46699]
      1. Human (Homo sapiens) [TaxId: 9606] [46700] (7) picpic
    6. Pit-1 POU homeodomain [46701]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [46702] (1) picpic
    7. Thyroid transcription factor 1 homeodomain [46703]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [46704] (1) picpic
    8. Oct-2 POU Homeodomain [46705]
      1. Human (Homo sapiens) [TaxId: 9606] [46706] (1) picpic
    9. Oct-3 POU Homeodomain [46707]
      1. Mouse (Mus musculus) [TaxId: 10090] [46708] (1) picpic
    10. Homeobox protein hox-b1 [46709]
      1. Human (Homo sapiens) [TaxId: 9606] [46710] (1) picpic
    11. Homeobox protein hox-a9 [100994]
      1. Mouse (Mus musculus) [TaxId: 10090] [100995] (1) picpic
    12. pbx1 [46711]
      1. Human (Homo sapiens) [TaxId: 9606] [46712] (2) picpic
      2. Mouse (Mus musculus) [TaxId: 10090] [46713] (2) picpic
    13. Insulin gene enhancer protein isl-1 [46714]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [46715] (1) picpic
    14. Msx-1 homeodomain [63463]
      1. Mouse (Mus musculus) [TaxId: 10090] [63464] (1) picpic
    15. Antennapedia Homeodomain [46716]
      1. Drosophila melanogaster [TaxId: 7227] [46717] (5) picpic
    16. Ultrabithorax (ubx) homeodomain [46718]
      1. Drosophila melanogaster [TaxId: 7227] [46719] (1) picpic
    17. Extradenticle (exd) homeodomain [46720]
      1. Drosophila melanogaster [TaxId: 7227] [46721] (3) picpic
    18. Even-skipped homeodomain [63465]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [63466] (1) picpic
    19. Fushi Tarazu protein [46722]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [46723] (1) picpic
    20. VND/NK-2 protein [46724]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [46725] (4) picpic
    21. Paired protein [46726]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [46727] (1) picpic
    22. Homeo-prospero domain of Prospero protein [81681]
      single domain composed of a homeodomain-homology N-terminal region (1245-1295) and the prospero-specific C-terminal region (1296-1396) that forms a 4-helical bundle
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [81682] (2) picpic
    23. Homeodomain-only protein, Hop [109647]
      1. Mouse (Mus musculus) [TaxId: 10090] [109648] (2) picpic
        SQ Q8R1H0
    24. ZF-HD homeobox protein At5g65410 [116772]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [116773] (1) picpic
        SQ Q9FKP8 182-248
    25. ZF-HD homeobox protein At4g24660 [116774]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [116775] (1) picpic
        SQ Q9SB61 148-215
    26. DNA-binding protein SATB2 [116776]
      1. Human (Homo sapiens) [TaxId: 9606] [116777] (1) picpic
        SQ Q9UPW6 615-672 # the structure of the 1st CUT domain (350-437) is also known: 1WIZ
    27. Homeobox-leucine zipper protein Homez [116778]
      1. Human (Homo sapiens) [TaxId: 9606] [116779] (1) picpic
        SQ Q8IX15 337-399
        Structural genomics target
    28. Hepatocyte nuclear factor 6 [116780]
      1. Mouse (Mus musculus) [TaxId: 10090] [116781] (1) picpic
        SQ O08755 291-437
    29. LAG1 longevity assurance homolog 5, LASS5 [140141]
      1. Mouse (Mus musculus) [TaxId: 10090] [140142] (1) picpic
        SQ Q9D6K9 77-135
    30. Paired box protein pax6 [140143]
      1. Human (Homo sapiens) [TaxId: 9606] [140144] (1) picpic
        SQ P26367 211-278
    31. Transcriptional adaptor 2-like, TADA2L, isoform b [140145]
      1. Human (Homo sapiens) [TaxId: 9606] [140146] (1) picpic
        SQ Q9BVJ0 72-118
    32. Lag1 longevity assurance homolog 6, LASS6 [140147]
      1. Mouse (Mus musculus) [TaxId: 10090] [140148] (1) picpic
        SQ Q8C172 76-127
    33. Homeobox protein prh [140149]
      1. Human (Homo sapiens) [TaxId: 9606] [140150] (1) picpic
        SQ Q03014 138-194
    34. Pituitary homeobox 2 [140151]
      1. Human (Homo sapiens) [TaxId: 9606] [140152] (1) picpic
        SQ Q99697 85-144
    35. Homeobox protein pknox1 [140153]
      1. Human (Homo sapiens) [TaxId: 9606] [140154] (1) picpic
        SQ P55347 257-318
    36. Homeotic bicoid protein [140155]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [140156] (1) picpic
        SQ P09081 97-163
    37. Hypothetical protein 4930532d21rik [140157]
      1. Mouse (Mus musculus) [TaxId: 10090] [140158] (1) picpic
        SQ Q8C0V1 712-760
    38. Homeobox-containing protein 1, HMBOX1 (Flj21616) [140159]
      1. Human (Homo sapiens) [TaxId: 9606] [140160] (1) picpic
        SQ Q6NT76 268-350
    39. Homeobox protein hox-b13 [140161]
      1. Human (Homo sapiens) [TaxId: 9606] [140162] (1) picpic
        SQ Q92826 216-273
    40. Zinc fingers and homeoboxes protein 1, ZHX1 [158242]
      1. Human (Homo sapiens) [TaxId: 9606] [158243] (1) picpic
        SQ Q9UKY1 565-640
  2. Recombinase DNA-binding domain [46728] (5)
    1. HIN recombinase (DNA-binding domain) [46729]
      1. Synthetic [46730] (8) picpic
    2. gamma,delta resolvase (C-terminal domain) [46731]
      1. Escherichia coli [TaxId: 562] [46732] (11) picpic
    3. Transposase tc3a1-65 [46733]
      1. Caenorhabditis elegans [TaxId: 6239] [46734] (2) picpic
        SQ P34257 2-104
    4. Ibeta subdomain of the mu end DNA-binding domain of phage mu transposase [46735]
      contains additional helix at each terminus
      1. Bacteriophage mu [TaxId: 10677] [46736] (2) picpic
    5. Transposase [46737]
      1. Bacteriophage mu [TaxId: 10677] [46738] (2) picpic
  3. Myb/SANT domain [46739] (15)
    1. c-Myb, DNA-binding domain [46740]
      duplication
      1. Mouse (Mus musculus) [TaxId: 10090] [46742] (16) picpic
    2. b-Myb DNA binding domain [46743]
      1. Chicken (Gallus gallus) [TaxId: 9031] [46744] (1) picpic
    3. v-Myb [68960]
      1. Avian myeloblastosis virus [TaxId: 11866] [68961] (1) picpic
    4. Rap1 [63467]
      1. Human (Homo sapiens) [TaxId: 9606] [63468] (1) picpic
    5. SANT domain of the nucleosome remodeling ATPase ISWI [100996]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [100997] (1) picpic
    6. 2610100b20rik gene product [109649]
      1. Mouse (Mus musculus) [TaxId: 10090] [109650] (1) picpic
        SQ Q80TB4 1951-2032
    7. Hypothetical protein C14orf106 (KIAA1903) [116782]
      1. Human (Homo sapiens) [TaxId: 9606] [116783] (1) picpic
        SQ Q6P0N0 877-936
    8. Metastasis associated protein MTA3 [140163]
      1. Mouse (Mus musculus) [TaxId: 10090] [140164] (1) picpic
        SQ Q924K8 267-323
    9. REST corepressor 1, CoREST [140165]
      1. Human (Homo sapiens) [TaxId: 9606] [140166] (2) picpic
        SQ Q9UKL0 376-440
    10. Radialis [140167]
      stand-alone Myb/SANT domain
      1. Garden snapdragon (Antirrhinum majus) [TaxId: 4151] [140168] (1) picpic
        SQ Q58FS3 8-70
    11. DnaJ homolog subfamily C member 1 [140169]
      1. Human (Homo sapiens) [TaxId: 9606] [140170] (2) picpic
        SQ Q96KC8 327-385! SQ Q96KC8 484-543
    12. Nuclear receptor corepressor 2 [140171]
      1. Human (Homo sapiens) [TaxId: 9606] [140172] (1) picpic
        SQ Q9Y618 413-480
    13. MYSM1 (KIAA1915) [140173]
      1. Human (Homo sapiens) [TaxId: 9606] [140174] (1) picpic
        SQ Q5VVJ2 117-181
    14. Telomere binding protein TBP1 [158244]
      1. Tobacco (Nicotiana tabacum) [TaxId: 4097] [158245] (3) picpic
        SQ Q84ZU4 578-660
    15. Telomere repeat-binding protein [158246]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [158247] (1) picpic
        SQ Q9LTI6 464-560
  4. SLIDE domain [100998] (1)
    myb-related probable DNA-binding motif
    1. SLIDE domain of the nucleosome remodeling ATPase ISWI [100999]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [101000] (1) picpic
  5. GARP response regulators [81683] (1)
    plant myb-related DNA-binding motif
    1. Arr10-B [81684]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [81685] (1) picpic
  6. DNA-binding domain of telomeric protein [46745] (2)
    part of Pfam 00249 (Myb/SANT domain)
    1. DNA-binding domain of human telomeric protein, hTRF1 [46746]
      1. Human (Homo sapiens) [TaxId: 9606] [46747] (4) picpic
        SQ P54274 379-430 # structure of dimerisation domain (62-265) is also known (scop_sp 63603)
    2. Telomeric repeat binding factor 2, TRF2 [116784]
      1. Human (Homo sapiens) [TaxId: 9606] [116785] (4) picpic
        SQ Q15554 446-500 # structure of dimerisation domain (43-245) is also known (scop_sp 63605)
  7. Paired domain [46748] (3)
    duplication: consists of two domains of this fold
    1. Pax-5 [68962]
      1. Human (Homo sapiens) [TaxId: 9606] [68963] (2) picpic
    2. Pax-6 [68936]
      1. Human (Homo sapiens) [TaxId: 9606] [46750] (1) picpic
    3. Paired protein (prd) [46751]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [46752] (1) picpic
  8. DNA-binding domain of rap1 [46753] (1)
    duplication: consist of two domains of this fold
    1. DNA-binding domain of rap1 [46754]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [46755] (1) picpic
  9. Centromere-binding [46756] (2)
    duplication: tandem repeat of two similar domains
    1. DNA-binding domain of centromere binding protein B (CENP-B) [46757]
      1. Human (Homo sapiens) [TaxId: 9606] [46758] (2) picpic
    2. Ars-binding protein 1, ABP1 [74670]
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [74671] (1) picpic
  10. FIS-like [100918] (4)
    1. FIS protein [48285]
      includes N-terminal dimerisation subdomain
      1. Escherichia coli [TaxId: 562] [48286] (12) picpic
    2. DNA-binding domain of NTRC [48287]
      includes N-terminal dimerisation subdomain
      1. Salmonella typhimurium [TaxId: 90371] [48288] (1) picpic
    3. Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain [101001]
      1. Rhodobacter sphaeroides [TaxId: 1063] [101002] (1) picpic
    4. Transcriptional regulator TyrR, C-terminal domain [63470]
      1. Haemophilus influenzae [TaxId: 727] [63471] (1) picpic
  11. AraC type transcriptional activator [46759] (2)
    duplication: consists of two structural repeats bipartite HTH protein
    1. MarA [46760]
      1. Escherichia coli [TaxId: 562] [46761] (1) picpic
    2. Rob transcription factor, N-terminal domain [46762]
      1. Escherichia coli [TaxId: 562] [46763] (1) picpic
  12. Tetracyclin repressor-like, N-terminal domain [46764] (34)
    1. Tetracyclin repressor (Tet-repressor, TetR) [46765]
      1. Escherichia coli [TaxId: 562] [46766] (13) picpic
    2. Multidrug binding protein QacR [68964]
      1. Staphylococcus aureus [TaxId: 1280] [68965] (47) picpic
        SQ P23217
    3. Hypothetical transcriptional regulator YcdC [88973]
      1. Escherichia coli [TaxId: 562] [88974] (1) picpic
    4. Hypothetical transcriptional regulator YsiA [101003]
      1. Bacillus subtilis [TaxId: 1423] [101004] (1) picpic
    5. Hypothetical transcriptional regulator YfiR [101005]
      1. Bacillus subtilis [TaxId: 1423] [101006] (1) picpic
    6. Ethr repressor [109651]
      1. Mycobacterium tuberculosis [TaxId: 1773] [109652] (3) picpic
        SQ P96222 22-215
    7. A-factor receptor homolog CprB [109653]
      gamma-butyrolactone receptor
      1. Streptomyces coelicolor [TaxId: 1902] [109654] (2) picpic
        SQ O66122
    8. Putative transcriptional repressor YbiH [109655]
      1. Salmonella typhimurium [TaxId: 90371] [109656] (1) picpic
        SQ Q8ZQN9
    9. Putative transcriptional regulator YxaF [109657]
      1. Bacillus subtilis [TaxId: 1423] [109658] (1) picpic
        SQ P42105
    10. Transcriptional regulator BC3163 [140175]
      1. Bacillus cereus [TaxId: 1396] [140176] (1) picpic
        SQ Q81BJ4 9-77
    11. Putative transcriptional regulator [140177]
      1. Rhodococcus sp. rha1 [TaxId: 101510] [140178] (2) picpic
    12. Putative transcriptional regulator SCO5951 [140179]
      1. Streptomyces coelicolor [TaxId: 1902] [140180] (2) picpic
        SQ O54180 13-80
    13. Transcriptional regulator Cgl2612 [140181]
      1. Corynebacterium glutamicum [TaxId: 1718] [140182] (4) picpic
        SQ Q8NMG3 1-174
    14. Transcriptional regulator EF0787 [140183]
      1. Enterococcus faecalis [TaxId: 1351] [140184] (2) picpic
        SQ Q837P6 4-71
    15. Putative transcriptional regulator RHA1_ro09068 [140185]
      1. Rhodococcus sp. [TaxId: 1831] [140186] (2) picpic
        SQ Q0RX74 10-78
    16. Probable transcriptional regulator PA3133 [140187]
      1. Pseudomonas aeruginosa [TaxId: 287] [140188] (1) picpic
        SQ Q9HZ91 1-76
    17. Transcriptional regulator RHA1_ro04179 [140189]
      1. Rhodococcus sp. [TaxId: 1831] [140190] (4) picpic
        SQ Q0S914 9-77
    18. Transcriptional regulator BC5000 [140191]
      1. Bacillus cereus [TaxId: 1396] [140192] (2) picpic
        SQ Q815X4 6-77
    19. Probable transcriptional regulator RHA1_ro04631 [140193]
      1. Rhodococcus sp. rha1 [TaxId: 101510] [140194] (2) picpic
        SQ Q0S7R9 4-80
    20. Putative transcriptional regulator Rha04620 [140195]
      1. Rhodococcus sp. rha1 [TaxId: 101510] [140196] (1) picpic
    21. Hemolysin II regulatory protein, HlyIIR [140197]
      1. Bacillus cereus [TaxId: 1396] [140198] (1) picpic
        SQ Q7X506 4-76
    22. Putative transcriptional regulator SCO7704 [140199]
      1. Streptomyces coelicolor [TaxId: 1902] [140200] (1) picpic
        SQ Q93JG8 16-83
    23. Probable transcriptional regulator PA1836 [140201]
      1. Pseudomonas aeruginosa [TaxId: 287] [140202] (1) picpic
        SQ Q9I2Q9 6-75
    24. Putative regulator SCO4008 [140203]
      1. Streptomyces coelicolor [TaxId: 1902] [140204] (2) picpic
        SQ Q9ADP7 7-74
    25. Transcriptional regulator PsrA [140205]
      1. Pseudomonas aeruginosa [TaxId: 287] [140206] (1) picpic
        SQ Q9HZJ9 2-80
    26. Putative transcriptional regulator SCO0857 [140207]
      1. Streptomyces coelicolor [TaxId: 1902] [140208] (2) picpic
        SQ Q9RCV4 35-99
    27. Transcriptional regulator TM1030 [140209]
      1. Thermotoga maritima [TaxId: 2336] [140210] (5) picpic
        SQ Q9X0C0 1-75! SQ Q9X0C0 2-75
    28. Putative transcriptional regulator Atu0279 [140211]
      1. Agrobacterium tumefaciens [TaxId: 358] [140212] (1) picpic
        SQ Q8UIL4 3-76
    29. Transcriptional activator DhaS [158248]
      1. Lactococcus lactis [TaxId: 1358] [158249] (2) picpic
        SQ Q9CIV9 8-78
    30. Putative transcriptional regulator SCO4940 [158250]
      1. Streptomyces coelicolor [TaxId: 1902] [158251] (1) picpic
        SQ Q8CJS4 8-82
    31. Putative transcriptional regulator RHA1_ro03468 [158252]
      1. Rhodococcus sp. RHA1 [TaxId: 101510] [158253] (2) picpic
        SQ Q0SB15 18-87
    32. Putative regulatory protein Sco4313 [158254]
      1. Streptomyces coelicolor [TaxId: 1902] [158255] (1) picpic
        SQ Q9KXS8 8-86
    33. Transcriptional regulator Cgl1640/Cg1846 [158256]
      1. Corynebacterium glutamicum [TaxId: 1718] [158257] (1) picpic
        SQ Q8NQ14 1-78
    34. Putative transcriptional regulator SCO4850 [158258]
      1. Streptomyces coelicolor [TaxId: 1902] [158259] (1) picpic
        SQ Q9KZ96 15-89
  13. Middle operon regulator, Mor [109659] (1)
    contains extra N-terminal dimerisation subdomain: alpha-hairpin (27-72) dimer is a four-helical bundle with right-handed twist
    1. Middle operon regulator, Mor [109660]
      1. Bacteriophage Mu [TaxId: 10677] [109661] (1) picpic
        SQ P23848 27-120
  14. Psq domain [140213] (1)
    Pfam 05225
    1. Ligand-dependent corepressor (LCoR) [140214]
      1. Human (Homo sapiens) [TaxId: 9606] [140215] (1) picpic
        SQ Q96JN0 343-405
  15. Alr1493-like [140216] (1)
    Pfam 04255; DUF433; contains extra C-terminal helix and N-terminal dimerisation interlock subdomain (scop_cf 47405)
    1. Hypothetical protein Ava_0674 (Alr1493 orthologue) [140217]
      1. Anabaena variabilis [TaxId: 1172] [140218] (2) picpic
        SQ Q3MFD8 1-102
  16. Nanomeric phage protein-like [140219] (1)
    contains additional N and C-terminal helices and the C-terminal beta-strand forming an intersubunit beta-barrel with a channel
    1. Phage protein BC1890 [140220]
      1. Bacillus cereus [TaxId: 1396] [140221] (6) picpic
        SQ Q81ES4 13-132
        host bacterium
  17. SWIRM domain [140222] (3)
    Pfam 04433; contains extra N-terminal helix
    1. Transcription regulatory protein swi3 [140223]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140224] (1) picpic
        SQ P32591 311-395
    2. Transcriptional adaptor 2-like, TADA2L [140225]
      1. Mouse (Mus musculus) [TaxId: 10090] [140226] (3) picpic
        SQ Q8CHV6 343-443! SQ Q8CHV6 355-443
    3. Lysine-specific histone demethylase 1, LSD1 [140227]
      1. Human (Homo sapiens) [TaxId: 9606] [140228] (9) picpic
        SQ O60341 169-279
  18. Cgl2762-like [158260] (1)
    Pfam 01527; Transposase 8
    1. Uncharacterized protein Cgl2762 [158261]
      1. Corynebacterium glutamicum [TaxId: 1718] [158262] (1) picpic
        SQ Q8NM20 1-89
  19. RpiR-like [158263] (1)
    Pfam 01418; contains two extra helices, one at each termini; overall arrangment of five helices is similar to the helical core of the lambda integrase-like catalytic domain (scop_fa 56350)
    1. Putative transcriptional regulator YbbH [158264]
      1. Bacillus subtilis [TaxId: 1423] [158265] (3) picpic
        SQ Q45581 1-83
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MRC site Generated from scop database 1.75 with scopm 1.101 on Wed Jun 3 10:42:06 2009
Copyright © 1994-2009 The scop authors / scop@mrc-lmb.cam.ac.uk