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O35744

- CHIL3_MOUSE

UniProt

O35744 - CHIL3_MOUSE

Protein

Chitinase-like protein 3

Gene

Chil3

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 111 (01 Oct 2014)
      Sequence version 2 (01 Mar 2001)
      Previous versions | rss
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    Functioni

    Lectin that binds saccharides with a free amino group, such as glucosamine or galactosamine. Binding to oligomeric saccharides is much stronger than binding to mono- or disaccharides. Also binds chitin and heparin. Has weak hexosaminidase activity but no chitinase activity. Has chemotactic activity for T-lymphocytes, bone marrow cells and eosinophils. May play a role in inflammation and allergy.3 Publications

    Catalytic activityi

    Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.1 Publication

    Kineticsi

    4-methylumbelliferone-N-acetylglucosamine (MU-(GlcNAc)1) is a GlcNAc2 analog.

    1. KM=120.8 µM for 4-methylumbelliferone-N-acetylglucosamine (at pH 4-4.5)1 Publication

    Vmax=0.023 µmol/min/mg enzyme1 Publication

    pH dependencei

    Optimum pH is 4.5-5.0.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei140 – 1401ChitooligosaccharideCurated
    Binding sitei213 – 2131ChitooligosaccharideCurated

    GO - Molecular functioni

    1. beta-N-acetylhexosaminidase activity Source: MGI
    2. carbohydrate binding Source: MGI
    3. chitin binding Source: UniProtKB-KW

    GO - Biological processi

    1. chitin catabolic process Source: InterPro
    2. inflammatory response Source: MGI
    3. polysaccharide catabolic process Source: UniProtKB-KW

    Keywords - Molecular functioni

    Glycosidase, Hydrolase

    Keywords - Biological processi

    Carbohydrate metabolism, Inflammatory response, Polysaccharide degradation

    Keywords - Ligandi

    Chitin-binding, Lectin

    Protein family/group databases

    CAZyiGH18. Glycoside Hydrolase Family 18.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Chitinase-like protein 3 (EC:3.2.1.52)
    Alternative name(s):
    Beta-N-acetylhexosaminidase Ym1
    Chitinase-3-like protein 3
    ECF-L
    Eosinophil chemotactic cytokine
    Secreted protein Ym1
    Gene namesi
    Name:Chil3
    Synonyms:Chi3l3, Ym1
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 3

    Organism-specific databases

    MGIiMGI:1330860. Chil3.

    Subcellular locationi

    Secreted. Rough endoplasmic reticulum lumen. Nucleus envelope. Cytoplasm. Cytoplasmic granule
    Note: Predominantly localizes to the lumen of rough endoplasmic reticulum (rER) and nuclear envelope in alveolar macrophages. Localizes to the dilated lumen of rER in immature neutrophils in spleen and in cytoplasmic granules in peritoneal neutrophils. Detected in needle-shaped crystals present in the cytoplasm of bone marrow macrophages.

    GO - Cellular componenti

    1. cytoplasm Source: MGI
    2. cytoplasmic membrane-bounded vesicle Source: MGI
    3. extracellular region Source: UniProtKB-SubCell
    4. nuclear envelope Source: UniProtKB-SubCell
    5. rough endoplasmic reticulum lumen Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm, Endoplasmic reticulum, Nucleus, Secreted

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 21212 PublicationsAdd
    BLAST
    Chaini22 – 398377Chitinase-like protein 3PRO_0000011970Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi26 ↔ 51
    Disulfide bondi49 ↔ 394
    Disulfide bondi307 ↔ 372

    Keywords - PTMi

    Disulfide bond

    Proteomic databases

    MaxQBiO35744.
    PaxDbiO35744.
    PRIDEiO35744.

    Expressioni

    Tissue specificityi

    Expressed in peritoneal cavity macrophages and in peritoneal and bone marrow-derived neutrophils. Abundantly expressed in bone marrow, with moderate levels detected in gastric antrum, spleen and in alveolar macrophages in lung. Not detected in brain, heart, liver, kidney, stomach, intestine, skeletal muscle, ovary, testis, thymus and lymph nodes (at protein level). Detected at low levels in bone marrow, spleen, thymus and lung. Barely detectable in intestine, kidney and coecum.6 Publications

    Developmental stagei

    In yolk sac, first detected at low levels at E8.5, with significant expression detected at E10.5 in myeloid precursor cells. In liver, expressed from E16.5 to P7.5 with highest levels detected from E18.5 to P0.5. In spleen, first detected at E16.5, with peak levels detected at E18.5 and P0.5 and expression persisting through the spleen maturation to the adult stage. In bone marrow, high expression levels detected from E16.5 until adulthood. In lung, first detected around the time of birth, with levels increasing significantly from P14.5 towards adulthood.1 Publication

    Inductioni

    Up-regulated in response to IL3 and IL4, during the inflammatory response and upon parasitic infection.4 Publications

    Gene expression databases

    ArrayExpressiO35744.
    BgeeiO35744.
    CleanExiMM_CHI3L3.
    GenevestigatoriO35744.

    Interactioni

    Protein-protein interaction databases

    IntActiO35744. 1 interaction.
    MINTiMINT-4090737.

    Structurei

    Secondary structure

    1
    398
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi23 – 297
    Helixi30 – 345
    Helixi37 – 393
    Helixi43 – 453
    Turni48 – 503
    Beta strandi52 – 6211
    Beta strandi65 – 673
    Helixi73 – 8210
    Helixi83 – 853
    Beta strandi91 – 977
    Turni99 – 1013
    Helixi104 – 1107
    Helixi113 – 12917
    Beta strandi134 – 1385
    Beta strandi142 – 1443
    Helixi150 – 17324
    Beta strandi179 – 1846
    Helixi188 – 1947
    Helixi197 – 2037
    Beta strandi205 – 2095
    Helixi217 – 2193
    Helixi236 – 2405
    Helixi243 – 25210
    Helixi257 – 2593
    Beta strandi260 – 27415
    Beta strandi284 – 2885
    Turni293 – 2953
    Beta strandi300 – 3023
    Helixi303 – 3119
    Beta strandi315 – 3195
    Turni320 – 3234
    Beta strandi324 – 3296
    Beta strandi332 – 3354
    Helixi339 – 35113
    Beta strandi356 – 3605
    Helixi362 – 3643
    Turni370 – 3723
    Helixi378 – 3869

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1E9LX-ray2.50A22-398[»]
    1VF8X-ray1.31A22-398[»]
    ProteinModelPortaliO35744.
    SMRiO35744. Positions 22-394.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO35744.

    Family & Domainsi

    Sequence similaritiesi

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiCOG3325.
    GeneTreeiENSGT00550000074323.
    HOGENOMiHOG000111109.
    HOVERGENiHBG011684.
    InParanoidiO35744.
    KOiK17524.
    OMAiIISYWKD.
    OrthoDBiEOG7ZGX3G.
    PhylomeDBiO35744.
    TreeFamiTF315610.

    Family and domain databases

    Gene3Di3.10.50.10. 1 hit.
    3.20.20.80. 2 hits.
    InterProiIPR011583. Chitinase_II.
    IPR029070. Chitinase_insertion.
    IPR001223. Glyco_hydro18cat.
    IPR013781. Glyco_hydro_catalytic_dom.
    IPR017853. Glycoside_hydrolase_SF.
    [Graphical view]
    PfamiPF00704. Glyco_hydro_18. 1 hit.
    [Graphical view]
    SMARTiSM00636. Glyco_18. 1 hit.
    [Graphical view]
    SUPFAMiSSF51445. SSF51445. 2 hits.
    SSF54556. SSF54556. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    O35744-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAKLILVTGL AILLNVQLGS SYQLMCYYTS WAKDRPIEGS FKPGNIDPCL    50
    CTHLIYAFAG MQNNEITYTH EQDLRDYEAL NGLKDKNTEL KTLLAIGGWK 100
    FGPAPFSAMV STPQNRQIFI QSVIRFLRQY NFDGLNLDWQ YPGSRGSPPK 150
    DKHLFSVLVK EMRKAFEEES VEKDIPRLLL TSTGAGIIDV IKSGYKIPEL 200
    SQSLDYIQVM TYDLHDPKDG YTGENSPLYK SPYDIGKSAD LNVDSIISYW 250
    KDHGAASEKL IVGFPAYGHT FILSDPSKTG IGAPTISTGP PGKYTDESGL 300
    LAYYEVCTFL NEGATEVWDA PQEVPYAYQG NEWVGYDNVR SFKLKAQWLK 350
    DNNLGGAVVW PLDMDDFSGS FCHQRHFPLT STLKGDLNIH SASCKGPY 398
    Length:398
    Mass (Da):44,458
    Last modified:March 1, 2001 - v2
    Checksum:iC11187661B99D1D1
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti105 – 1051P → S no nucleotide entry (PubMed:9828134)Curated
    Sequence conflicti105 – 1051P → S in BAA13458. (PubMed:10625674)Curated
    Sequence conflicti257 – 2571S → P in BAE23385. (PubMed:11297523)Curated
    Sequence conflicti361 – 3611P → R no nucleotide entry (PubMed:9828134)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D87757 mRNA. Translation: BAA13458.2.
    M94584 mRNA. Translation: AAB62394.2.
    AK137503 mRNA. Translation: BAE23385.1.
    AK154420 mRNA. Translation: BAE32572.1.
    BC061154 mRNA. Translation: AAH61154.1.
    U56900 mRNA. Translation: AAB01230.1.
    CCDSiCCDS17718.1.
    PIRiS27879.
    RefSeqiNP_034022.2. NM_009892.2.
    UniGeneiMm.387173.

    Genome annotation databases

    EnsembliENSMUST00000063062; ENSMUSP00000053923; ENSMUSG00000040809.
    GeneIDi12655.
    KEGGimmu:12655.
    UCSCiuc008qvw.2. mouse.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D87757 mRNA. Translation: BAA13458.2 .
    M94584 mRNA. Translation: AAB62394.2 .
    AK137503 mRNA. Translation: BAE23385.1 .
    AK154420 mRNA. Translation: BAE32572.1 .
    BC061154 mRNA. Translation: AAH61154.1 .
    U56900 mRNA. Translation: AAB01230.1 .
    CCDSi CCDS17718.1.
    PIRi S27879.
    RefSeqi NP_034022.2. NM_009892.2.
    UniGenei Mm.387173.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1E9L X-ray 2.50 A 22-398 [» ]
    1VF8 X-ray 1.31 A 22-398 [» ]
    ProteinModelPortali O35744.
    SMRi O35744. Positions 22-394.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi O35744. 1 interaction.
    MINTi MINT-4090737.

    Chemistry

    ChEMBLi CHEMBL1795141.

    Protein family/group databases

    CAZyi GH18. Glycoside Hydrolase Family 18.

    Proteomic databases

    MaxQBi O35744.
    PaxDbi O35744.
    PRIDEi O35744.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000063062 ; ENSMUSP00000053923 ; ENSMUSG00000040809 .
    GeneIDi 12655.
    KEGGi mmu:12655.
    UCSCi uc008qvw.2. mouse.

    Organism-specific databases

    CTDi 12655.
    MGIi MGI:1330860. Chil3.

    Phylogenomic databases

    eggNOGi COG3325.
    GeneTreei ENSGT00550000074323.
    HOGENOMi HOG000111109.
    HOVERGENi HBG011684.
    InParanoidi O35744.
    KOi K17524.
    OMAi IISYWKD.
    OrthoDBi EOG7ZGX3G.
    PhylomeDBi O35744.
    TreeFami TF315610.

    Miscellaneous databases

    EvolutionaryTracei O35744.
    NextBioi 281876.
    PROi O35744.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi O35744.
    Bgeei O35744.
    CleanExi MM_CHI3L3.
    Genevestigatori O35744.

    Family and domain databases

    Gene3Di 3.10.50.10. 1 hit.
    3.20.20.80. 2 hits.
    InterProi IPR011583. Chitinase_II.
    IPR029070. Chitinase_insertion.
    IPR001223. Glyco_hydro18cat.
    IPR013781. Glyco_hydro_catalytic_dom.
    IPR017853. Glycoside_hydrolase_SF.
    [Graphical view ]
    Pfami PF00704. Glyco_hydro_18. 1 hit.
    [Graphical view ]
    SMARTi SM00636. Glyco_18. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51445. SSF51445. 2 hits.
    SSF54556. SSF54556. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Genetic characterization of the murine Ym1 gene and identification of a cluster of highly homologous genes."
      Jin H.M., Copeland N.G., Gilbert D.J., Jenkins N.A., Kirkpatrick R.B., Rosenberg M.
      Genomics 54:316-322(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], TISSUE SPECIFICITY.
      Strain: 129/SvJ.
    2. "Identification of a novel eosinophil chemotactic cytokine (ECF-L) as a chitinase family protein."
      Owhashi M., Arita H., Hayai N.
      J. Biol. Chem. 275:1279-1286(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 22-39, FUNCTION, TISSUE SPECIFICITY, INDUCTION.
      Tissue: Bone marrow.
    3. "A macrophage protein, Ym1, transiently expressed during inflammation is a novel mammalian lectin."
      Chang N.-C.A., Hung S.-I., Hwa K.-Y., Kato I., Chen J.-E., Liu C.-H., Chang A.C.
      J. Biol. Chem. 276:17497-17506(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 22-48; 109-134; 162-192 AND 210-225, FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INDUCTION.
      Tissue: Macrophage.
    4. "The transcriptional landscape of the mammalian genome."
      Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
      , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
      Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: NOD.
      Tissue: Bone and Dendritic cell.
    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].
      Tissue: Heart and Lung.
    6. "Mouse chitinase-related protein mRNA (MCRP), partial cds."
      Shmelkov S.V., Zinovjeva M.V., Belyavsky A.V.
      Submitted (APR-1996) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 139-398.
      Strain: CBA.
      Tissue: Bone marrow.
    7. "Ym1 is a neutrophil granule protein that crystallizes in p47phox-deficient mice."
      Harbord M., Novelli M., Canas B., Power D., Davis C., Godovac-Zimmermann J., Roes J., Segal A.W.
      J. Biol. Chem. 277:5468-5475(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
    8. "TH2 cytokines and allergic challenge induce Ym1 expression in macrophages by a STAT6-dependent mechanism."
      Welch J.S., Escoubet-Lozach L., Sykes D.B., Liddiard K., Greaves D.R., Glass C.K.
      J. Biol. Chem. 277:42821-42829(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION BY IL3 AND IL4.
    9. "Transient expression of Ym1, a heparin-binding lectin, during developmental hematopoiesis and inflammation."
      Hung S.I., Chang A.C., Kato I., Chang N.C.
      J. Leukoc. Biol. 72:72-82(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, INDUCTION.
    10. "Cellular expression of murine Ym1 and Ym2, chitinase family proteins, as revealed by in situ hybridization and immunohistochemistry."
      Nio J., Fujimoto W., Konno A., Kon Y., Owhashi M., Iwanaga T.
      Histochem. Cell Biol. 121:473-482(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
    11. "The crystal structure of a novel mammalian lectin, Ym1, suggests a saccharide binding site."
      Sun Y.-J., Chang N.-C.A., Hung S.-I., Chang A.C., Chou C.-C., Hsiao C.-D.
      J. Biol. Chem. 276:17507-17514(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 22-398, DISULFIDE BONDS.
    12. "The crystal structure of Ym1 at 1.31 A resolution."
      Tsai M.L., Liaw S.H., Chang N.C.
      J. Struct. Biol. 148:290-296(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.31 ANGSTROMS) OF 22-398, DISULFIDE BONDS.

    Entry informationi

    Entry nameiCHIL3_MOUSE
    AccessioniPrimary (citable) accession number: O35744
    Secondary accession number(s): P70201
    , Q3U462, Q3UV87, Q61201
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 16, 2004
    Last sequence update: March 1, 2001
    Last modified: October 1, 2014
    This is version 111 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Glycosyl hydrolases
      Classification of glycosyl hydrolase families and list of entries
    2. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3