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Q96BZ9

- TBC20_HUMAN

UniProt

Q96BZ9 - TBC20_HUMAN

Protein

TBC1 domain family member 20

Gene

TBC1D20

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
    • BLAST
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    • History
      Entry version 99 (01 Oct 2014)
      Sequence version 1 (01 Dec 2001)
      Previous versions | rss
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    Functioni

    GTPase-activating protein specific for Rab1 and Rab2 small GTPase families for which it can accelerate the intrinsic GTP hydrolysis rate by more than five orders of magnitude.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei105 – 1051Arginine finger
    Sitei144 – 1441Glutamine finger

    GO - Molecular functioni

    1. protein binding Source: IntAct
    2. Rab GTPase activator activity Source: InterPro

    GO - Biological processi

    1. viral process Source: UniProtKB-KW

    Keywords - Molecular functioni

    GTPase activation

    Keywords - Biological processi

    Host-virus interaction

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    TBC1 domain family member 20
    Gene namesi
    Name:TBC1D20
    Synonyms:C20orf140
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 20

    Organism-specific databases

    HGNCiHGNC:16133. TBC1D20.

    Subcellular locationi

    GO - Cellular componenti

    1. integral component of membrane Source: UniProtKB-KW

    Keywords - Cellular componenti

    Membrane

    Pathology & Biotechi

    Involvement in diseasei

    Warburg micro syndrome 4 (WARBM4) [MIM:615663]: A form of Warburg micro syndrome, a rare syndrome characterized by microcephaly, microphthalmia, microcornia, congenital cataracts, optic atrophy, cortical dysplasia, in particular corpus callosum hypoplasia, severe mental retardation, spastic diplegia, and hypogonadism.1 Publication
    Note: The disease is caused by mutations affecting the gene represented in this entry.

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi105 – 1051R → A: 1000-fold decrease in GAP activity. 1 Publication
    Mutagenesisi144 – 1441Q → L: 1000-fold decrease in GAP activity. 1 Publication

    Organism-specific databases

    MIMi615663. phenotype.
    Orphaneti2510. Micro syndrome.
    PharmGKBiPA25683.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 403403TBC1 domain family member 20PRO_0000208048Add
    BLAST

    Proteomic databases

    MaxQBiQ96BZ9.
    PaxDbiQ96BZ9.
    PRIDEiQ96BZ9.

    PTM databases

    PhosphoSiteiQ96BZ9.

    Expressioni

    Gene expression databases

    ArrayExpressiQ96BZ9.
    BgeeiQ96BZ9.
    CleanExiHS_TBC1D20.
    GenevestigatoriQ96BZ9.

    Organism-specific databases

    HPAiHPA043613.

    Interactioni

    Subunit structurei

    Directly interacts with the N-terminal amphipathic helix of hepatitis C virus (HCV) NS5A.2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    P2795811EBI-9254454,EBI-8753518From a different organism.

    Protein-protein interaction databases

    BioGridi126139. 4 interactions.
    IntActiQ96BZ9. 1 interaction.
    STRINGi9606.ENSP00000346139.

    Structurei

    Secondary structure

    1
    403
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi26 – 4015
    Beta strandi42 – 443
    Helixi47 – 559
    Turni57 – 604
    Helixi63 – 7311
    Helixi89 – 924
    Helixi96 – 1049
    Helixi105 – 1095
    Beta strandi112 – 1143
    Helixi116 – 13621
    Helixi146 – 15712
    Helixi159 – 17113
    Turni172 – 1754
    Helixi176 – 1783
    Beta strandi180 – 1823
    Turni184 – 1863
    Helixi187 – 1915
    Helixi192 – 1998
    Helixi201 – 2077
    Helixi215 – 2173
    Helixi218 – 2225
    Turni223 – 2286
    Helixi232 – 24413
    Helixi249 – 26012
    Helixi262 – 2665
    Helixi274 – 2807
    Helixi288 – 30114

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4HL4X-ray2.20A14-305[»]
    4HLQX-ray3.30A/C/E/G/I1-305[»]
    ProteinModelPortaliQ96BZ9.
    SMRiQ96BZ9. Positions 25-305.
    ModBaseiSearch...
    MobiDBiSearch...

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei238 – 25821HelicalSequence AnalysisAdd
    BLAST
    Transmembranei367 – 38721HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini60 – 246187Rab-GAP TBCPROSITE-ProRule annotationAdd
    BLAST

    Domaini

    The arginine and glutamine fingers are critical for the GTPase-activating mechanism, they pull out Rab's 'switch 2' glutamine and insert in Rab's active site.1 Publication

    Sequence similaritiesi

    Contains 1 Rab-GAP TBC domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiCOG5210.
    HOGENOMiHOG000006927.
    HOVERGENiHBG056376.
    OMAiLECECDM.
    OrthoDBiEOG7N63MJ.
    PhylomeDBiQ96BZ9.
    TreeFamiTF105942.

    Family and domain databases

    InterProiIPR000195. Rab-GTPase-TBC_dom.
    [Graphical view]
    PfamiPF00566. RabGAP-TBC. 1 hit.
    [Graphical view]
    SMARTiSM00164. TBC. 1 hit.
    [Graphical view]
    SUPFAMiSSF47923. SSF47923. 2 hits.
    PROSITEiPS50086. TBC_RABGAP. 1 hit.
    [Graphical view]

    Sequences (3)i

    Sequence statusi: Complete.

    This entry describes 3 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q96BZ9-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MALRSAQGDG PTSGHWDGGA EKADFNAKRK KKVAEIHQAL NSDPTDVAAL    50
    RRMAISEGGL LTDEIRRKVW PKLLNVNAND PPPISGKNLR QMSKDYQQVL 100
    LDVRRSLRRF PPGMPEEQRE GLQEELIDII LLILERNPQL HYYQGYHDIV 150
    VTFLLVVGER LATSLVEKLS THHLRDFMDP TMDNTKHILN YLMPIIDQVN 200
    PELHDFMQSA EVGTIFALSW LITWFGHVLS DFRHVVRLYD FFLACHPLMP 250
    IYFAAVIVLY REQEVLDCDC DMASVHHLLS QIPQDLPYET LISRAGDLFV 300
    QFPPSELARE AAAQQQAERT AASTFKDFEL ASAQQRPDMV LRQRFRGLLR 350
    PEDRTKDVLT KPRTNRFVKL AVMGLTVALG AAALAVVKSA LEWAPKFQLQ 400
    LFP 403
    Length:403
    Mass (Da):45,855
    Last modified:December 1, 2001 - v1
    Checksum:i70B011A33DEF527D
    GO
    Isoform 2 (identifier: Q96BZ9-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-192: Missing.
         209-364: SAEVGTIFAL...TKDVLTKPRT → RYICVCISVC...LANASFFKIF
         365-403: Missing.

    Note: May be due to intron retention. No experimental confirmation available.

    Show »
    Length:172
    Mass (Da):19,381
    Checksum:iD2D5BE89785800C6
    GO
    Isoform 3 (identifier: Q96BZ9-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-1: M → MPSGCYVPRSEPRLLPAPPPAGARVG

    Note: No experimental confirmation available.

    Show »
    Length:428
    Mass (Da):48,382
    Checksum:i6D826FCBCF5A491A
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti117 – 1171E → G in BAC86808. (PubMed:14702039)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti79 – 791N → S.
    Corresponds to variant rs36088178 [ dbSNP | Ensembl ].
    VAR_052543

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 192192Missing in isoform 2. 1 PublicationVSP_008100Add
    BLAST
    Alternative sequencei1 – 11M → MPSGCYVPRSEPRLLPAPPP AGARVG in isoform 3. 1 PublicationVSP_031524
    Alternative sequencei209 – 364156SAEVG…TKPRT → RYICVCISVCMHTHAHTPPH LKHSSQAERSFLIVLGGFVK FSPVVPVTSNLGNSVLGAFL GTVLFGGHSPSLEFTSSGER WIRYVCQGKMLRLLPQEKHK VLWDPVARRGRPTMGCFISQ VPKRRNIFLQIPCDVLFLLC LVGNVFLANASFFKIF in isoform 2. 1 PublicationVSP_008101Add
    BLAST
    Alternative sequencei365 – 40339Missing in isoform 2. 1 PublicationVSP_008102Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB449906 mRNA. Translation: BAH16649.1.
    AK055573 mRNA. No translation available.
    AK127062 mRNA. Translation: BAC86808.1.
    AK291648 mRNA. Translation: BAF84337.1.
    AL121747, AL049761 Genomic DNA. Translation: CAI23015.1.
    AL049761, AL121747 Genomic DNA. Translation: CAI23048.1.
    CH471133 Genomic DNA. Translation: EAX10670.1.
    BC014983 mRNA. No translation available.
    CCDSiCCDS13002.1. [Q96BZ9-1]
    RefSeqiNP_653229.1. NM_144628.3. [Q96BZ9-1]
    XP_005260718.1. XM_005260661.1. [Q96BZ9-1]
    UniGeneiHs.590876.

    Genome annotation databases

    EnsembliENST00000354200; ENSP00000346139; ENSG00000125875. [Q96BZ9-1]
    ENST00000461304; ENSP00000432280; ENSG00000125875. [Q96BZ9-1]
    GeneIDi128637.
    KEGGihsa:128637.
    UCSCiuc002wds.3. human. [Q96BZ9-1]

    Polymorphism databases

    DMDMi34395569.

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB449906 mRNA. Translation: BAH16649.1 .
    AK055573 mRNA. No translation available.
    AK127062 mRNA. Translation: BAC86808.1 .
    AK291648 mRNA. Translation: BAF84337.1 .
    AL121747 , AL049761 Genomic DNA. Translation: CAI23015.1 .
    AL049761 , AL121747 Genomic DNA. Translation: CAI23048.1 .
    CH471133 Genomic DNA. Translation: EAX10670.1 .
    BC014983 mRNA. No translation available.
    CCDSi CCDS13002.1. [Q96BZ9-1 ]
    RefSeqi NP_653229.1. NM_144628.3. [Q96BZ9-1 ]
    XP_005260718.1. XM_005260661.1. [Q96BZ9-1 ]
    UniGenei Hs.590876.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4HL4 X-ray 2.20 A 14-305 [» ]
    4HLQ X-ray 3.30 A/C/E/G/I 1-305 [» ]
    ProteinModelPortali Q96BZ9.
    SMRi Q96BZ9. Positions 25-305.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 126139. 4 interactions.
    IntActi Q96BZ9. 1 interaction.
    STRINGi 9606.ENSP00000346139.

    PTM databases

    PhosphoSitei Q96BZ9.

    Polymorphism databases

    DMDMi 34395569.

    Proteomic databases

    MaxQBi Q96BZ9.
    PaxDbi Q96BZ9.
    PRIDEi Q96BZ9.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000354200 ; ENSP00000346139 ; ENSG00000125875 . [Q96BZ9-1 ]
    ENST00000461304 ; ENSP00000432280 ; ENSG00000125875 . [Q96BZ9-1 ]
    GeneIDi 128637.
    KEGGi hsa:128637.
    UCSCi uc002wds.3. human. [Q96BZ9-1 ]

    Organism-specific databases

    CTDi 128637.
    GeneCardsi GC20M000416.
    HGNCi HGNC:16133. TBC1D20.
    HPAi HPA043613.
    MIMi 611663. gene.
    615663. phenotype.
    neXtProti NX_Q96BZ9.
    Orphaneti 2510. Micro syndrome.
    PharmGKBi PA25683.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG5210.
    HOGENOMi HOG000006927.
    HOVERGENi HBG056376.
    OMAi LECECDM.
    OrthoDBi EOG7N63MJ.
    PhylomeDBi Q96BZ9.
    TreeFami TF105942.

    Miscellaneous databases

    ChiTaRSi TBC1D20. human.
    GenomeRNAii 128637.
    NextBioi 82406.
    PROi Q96BZ9.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q96BZ9.
    Bgeei Q96BZ9.
    CleanExi HS_TBC1D20.
    Genevestigatori Q96BZ9.

    Family and domain databases

    InterProi IPR000195. Rab-GTPase-TBC_dom.
    [Graphical view ]
    Pfami PF00566. RabGAP-TBC. 1 hit.
    [Graphical view ]
    SMARTi SM00164. TBC. 1 hit.
    [Graphical view ]
    SUPFAMi SSF47923. SSF47923. 2 hits.
    PROSITEi PS50086. TBC_RABGAP. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Identification and characterization of a novel Tre-2/Bub2/Cdc16 (TBC) protein that possesses Rab3A-GAP activity."
      Ishibashi K., Kanno E., Itoh T., Fukuda M.
      Genes Cells 14:41-52(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
      Tissue: Brain.
    2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 2 AND 3).
      Tissue: Brain, Lung and Placenta.
    3. "The DNA sequence and comparative analysis of human chromosome 20."
      Deloukas P., Matthews L.H., Ashurst J.L., Burton J., Gilbert J.G.R., Jones M., Stavrides G., Almeida J.P., Babbage A.K., Bagguley C.L., Bailey J., Barlow K.F., Bates K.N., Beard L.M., Beare D.M., Beasley O.P., Bird C.P., Blakey S.E.
      , Bridgeman A.M., Brown A.J., Buck D., Burrill W.D., Butler A.P., Carder C., Carter N.P., Chapman J.C., Clamp M., Clark G., Clark L.N., Clark S.Y., Clee C.M., Clegg S., Cobley V.E., Collier R.E., Connor R.E., Corby N.R., Coulson A., Coville G.J., Deadman R., Dhami P.D., Dunn M., Ellington A.G., Frankland J.A., Fraser A., French L., Garner P., Grafham D.V., Griffiths C., Griffiths M.N.D., Gwilliam R., Hall R.E., Hammond S., Harley J.L., Heath P.D., Ho S., Holden J.L., Howden P.J., Huckle E., Hunt A.R., Hunt S.E., Jekosch K., Johnson C.M., Johnson D., Kay M.P., Kimberley A.M., King A., Knights A., Laird G.K., Lawlor S., Lehvaeslaiho M.H., Leversha M.A., Lloyd C., Lloyd D.M., Lovell J.D., Marsh V.L., Martin S.L., McConnachie L.J., McLay K., McMurray A.A., Milne S.A., Mistry D., Moore M.J.F., Mullikin J.C., Nickerson T., Oliver K., Parker A., Patel R., Pearce T.A.V., Peck A.I., Phillimore B.J.C.T., Prathalingam S.R., Plumb R.W., Ramsay H., Rice C.M., Ross M.T., Scott C.E., Sehra H.K., Shownkeen R., Sims S., Skuce C.D., Smith M.L., Soderlund C., Steward C.A., Sulston J.E., Swann R.M., Sycamore N., Taylor R., Tee L., Thomas D.W., Thorpe A., Tracey A., Tromans A.C., Vaudin M., Wall M., Wallis J.M., Whitehead S.L., Whittaker P., Willey D.L., Williams L., Williams S.A., Wilming L., Wray P.W., Hubbard T., Durbin R.M., Bentley D.R., Beck S., Rogers J.
      Nature 414:865-871(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Skin.
    6. "A Rab-GAP TBC domain protein binds hepatitis C virus NS5A and mediates viral replication."
      Sklan E.H., Staschke K., Oakes T.M., Elazar M., Winters M., Aroeti B., Danieli T., Glenn J.S.
      J. Virol. 81:11096-11105(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH HCV NS5A.
    7. Cited for: INVOLVEMENT IN WARBM4.
    8. "Catalytic mechanism of a mammalian Rab.RabGAP complex in atomic detail."
      Gavriljuk K., Gazdag E.M., Itzen A., Kotting C., Goody R.S., Gerwert K.
      Proc. Natl. Acad. Sci. U.S.A. 109:21348-21353(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 14-305 ALONE AND IN COMPLEX WITH RAB1B, MUTAGENESIS OF ARG-105 AND GLN-144.

    Entry informationi

    Entry nameiTBC20_HUMAN
    AccessioniPrimary (citable) accession number: Q96BZ9
    Secondary accession number(s): A8K6I3
    , B9A6M1, Q5JWQ7, Q6ZSY8, Q96NE1, Q9BYM7, Q9H140
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 29, 2003
    Last sequence update: December 1, 2001
    Last modified: October 1, 2014
    This is version 99 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 20
      Human chromosome 20: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3