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O43837

- IDH3B_HUMAN

UniProt

O43837 - IDH3B_HUMAN

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Protein
Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
Gene
IDH3B
Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Catalytic activityi

Isocitrate + NAD+ = 2-oxoglutarate + CO2 + NADH.

Cofactori

Binds 1 magnesium or manganese ion per subunit By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei133 – 1331Substrate By similarity
Binding sitei164 – 1641Substrate By similarity
Sitei171 – 1711Critical for catalysis By similarity
Sitei218 – 2181Critical for catalysis By similarity
Metal bindingi251 – 2511Magnesium or manganese By similarity
Binding sitei251 – 2511Substrate By similarity

GO - Molecular functioni

  1. NAD binding Source: InterPro
  2. electron carrier activity Source: UniProtKB
  3. isocitrate dehydrogenase (NAD+) activity Source: ProtInc
  4. magnesium ion binding Source: InterPro

GO - Biological processi

  1. 2-oxoglutarate metabolic process Source: Ensembl
  2. NADH metabolic process Source: Ensembl
  3. cellular metabolic process Source: Reactome
  4. isocitrate metabolic process Source: ProtInc
  5. small molecule metabolic process Source: Reactome
  6. tricarboxylic acid cycle Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Tricarboxylic acid cycle

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, NAD

Enzyme and pathway databases

BioCyciMetaCyc:ENSG00000101365-MONOMER.
ReactomeiREACT_1785. Citric acid cycle (TCA cycle).
SABIO-RKO43837.

Names & Taxonomyi

Protein namesi
Recommended name:
Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial (EC:1.1.1.41)
Alternative name(s):
Isocitric dehydrogenase subunit beta
NAD(+)-specific ICDH subunit beta
Gene namesi
Name:IDH3B
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 20

Organism-specific databases

HGNCiHGNC:5385. IDH3B.

Subcellular locationi

GO - Cellular componenti

  1. mitochondrial matrix Source: Reactome
  2. mitochondrion Source: HPA
  3. nucleus Source: UniProt
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Involvement in diseasei

Retinitis pigmentosa 46 (RP46) [MIM:612572]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well.
Note: The disease is caused by mutations affecting the gene represented in this entry.1 Publication
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti132 – 1321L → P in RP46. 1 Publication
VAR_054851

Keywords - Diseasei

Disease mutation, Retinitis pigmentosa

Organism-specific databases

MIMi612572. phenotype.
Orphaneti791. Retinitis pigmentosa.
PharmGKBiPA29633.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 3434Mitochondrion By similarity
Add
BLAST
Chaini35 – 385351Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
PRO_0000014444Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei199 – 1991N6-acetyllysine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiO43837.
PaxDbiO43837.
PRIDEiO43837.

PTM databases

PhosphoSiteiO43837.

Expressioni

Gene expression databases

ArrayExpressiO43837.
BgeeiO43837.
CleanExiHS_IDH3B.
GenevestigatoriO43837.

Organism-specific databases

HPAiHPA049387.
HPA054180.

Interactioni

Subunit structurei

Heterooligomer of subunits alpha, beta, and gamma in the apparent ratio of 2:1:1 By similarity.

Protein-protein interaction databases

BioGridi109646. 7 interactions.
IntActiO43837. 6 interactions.
MINTiMINT-5003855.
STRINGi9606.ENSP00000370223.

Structurei

3D structure databases

ProteinModelPortaliO43837.
SMRiO43837. Positions 47-382.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0473.
HOVERGENiHBG052080.
InParanoidiO43837.
KOiK00030.
OMAiILATPDY.
OrthoDBiEOG75B85R.
PhylomeDBiO43837.
TreeFamiTF315033.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR004434. Isocitrate_DH_NAD.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PANTHERiPTHR11835. PTHR11835. 1 hit.
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00175. mito_nad_idh. 1 hit.
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

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

This entry describes 3 isoformsi produced by alternative splicing. Align

Isoform B (identifier: O43837-1) [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

MAALSGVRWL TRALVSAGNP GAWRGLSTSA AAHAASRSQA EDVRVEGSFP    50
VTMLPGDGVG PELMHAVKEV FKAAAVPVEF QEHHLSEVQN MASEEKLEQV 100
LSSMKENKVA IIGKIHTPME YKGELASYDM RLRRKLDLFA NVVHVKSLPG 150
YMTRHNNLDL VIIREQTEGE YSSLEHESAR GVIECLKIVT RAKSQRIAKF 200
AFDYATKKGR GKVTAVHKAN IMKLGDGLFL QCCEEVAELY PKIKFETMII 250
DNCCMQLVQN PYQFDVLVMP NLYGNIIDNL AAGLVGGAGV VPGESYSAEY 300
AVFETGARHP FAQAVGRNIA NPTAMLLSAS NMLRHLNLEY HSSMIADAVK 350
KVIKVGKVRT RDMGGYSTTT DFIKSVIGHL QTKGS 385
Length:385
Mass (Da):42,184
Last modified:May 1, 2007 - v2
Checksum:i7324E6CC30A68EE2
GO
Isoform A (identifier: O43837-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     361-385: RDMGGYSTTTDFIKSVIGHLQTKGS → SDMGGYATCHDFTEAVIAALPHP

Show »
Length:383
Mass (Da):41,887
Checksum:i6B5A3D3F82CCDB34
GO
Isoform C (identifier: O43837-3) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-177: MAALSGVRWL...EGEYSSLEHE → MKMGERWSSLFPFPVSPSCCFLLTQ

Show »
Length:233
Mass (Da):25,555
Checksum:i7036C0A641A17E2D
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti3 – 31A → V.1 Publication
Corresponds to variant rs3178817 [ dbSNP | Ensembl ].
VAR_022660
Natural varianti132 – 1321L → P in RP46. 1 Publication
VAR_054851
Natural varianti166 – 1661Q → H.
Corresponds to variant rs11542741 [ dbSNP | Ensembl ].
VAR_049781
Natural varianti360 – 3601T → A.
Corresponds to variant rs8296 [ dbSNP | Ensembl ].
VAR_056005

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 177177MAALS…SLEHE → MKMGERWSSLFPFPVSPSCC FLLTQ in isoform C.
VSP_041335Add
BLAST
Alternative sequencei361 – 38525RDMGG…QTKGS → SDMGGYATCHDFTEAVIAAL PHP in isoform A.
VSP_002462Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti127 – 1304SYDM → RTLV in CAB43266. 1 Publication
Sequence conflicti250 – 2501I → V in BAA91971. 1 Publication
Sequence conflicti385 – 3851S → SNL in AAD09340. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U49283 mRNA. Translation: AAB94295.1.
AF023265 mRNA. Translation: AAD09339.1.
AF023266 mRNA. Translation: AAD09340.1.
AK001905 mRNA. Translation: BAA91971.1.
AK315641 mRNA. Translation: BAG38008.1.
AL049712 Genomic DNA. Translation: CAC01442.2.
AL049712 Genomic DNA. Translation: CAC01443.1.
CH471133 Genomic DNA. Translation: EAX10579.1.
CH471133 Genomic DNA. Translation: EAX10580.1.
CH471133 Genomic DNA. Translation: EAX10582.1.
CH471133 Genomic DNA. Translation: EAX10583.1.
BC001960 mRNA. Translation: AAH01960.1.
AL050094 mRNA. Translation: CAB43266.1.
CCDSiCCDS13031.1. [O43837-2]
CCDS13032.1. [O43837-1]
PIRiT08743.
T13147.
RefSeqiNP_008830.2. NM_006899.3. [O43837-1]
NP_777280.1. NM_174855.2. [O43837-2]
UniGeneiHs.436405.

Genome annotation databases

EnsembliENST00000380843; ENSP00000370223; ENSG00000101365. [O43837-1]
ENST00000380851; ENSP00000370232; ENSG00000101365. [O43837-2]
GeneIDi3420.
KEGGihsa:3420.
UCSCiuc002wgp.4. human. [O43837-1]
uc002wgq.4. human. [O43837-2]
uc002wgr.4. human. [O43837-3]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U49283 mRNA. Translation: AAB94295.1 .
AF023265 mRNA. Translation: AAD09339.1 .
AF023266 mRNA. Translation: AAD09340.1 .
AK001905 mRNA. Translation: BAA91971.1 .
AK315641 mRNA. Translation: BAG38008.1 .
AL049712 Genomic DNA. Translation: CAC01442.2 .
AL049712 Genomic DNA. Translation: CAC01443.1 .
CH471133 Genomic DNA. Translation: EAX10579.1 .
CH471133 Genomic DNA. Translation: EAX10580.1 .
CH471133 Genomic DNA. Translation: EAX10582.1 .
CH471133 Genomic DNA. Translation: EAX10583.1 .
BC001960 mRNA. Translation: AAH01960.1 .
AL050094 mRNA. Translation: CAB43266.1 .
CCDSi CCDS13031.1. [O43837-2 ]
CCDS13032.1. [O43837-1 ]
PIRi T08743.
T13147.
RefSeqi NP_008830.2. NM_006899.3. [O43837-1 ]
NP_777280.1. NM_174855.2. [O43837-2 ]
UniGenei Hs.436405.

3D structure databases

ProteinModelPortali O43837.
SMRi O43837. Positions 47-382.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 109646. 7 interactions.
IntActi O43837. 6 interactions.
MINTi MINT-5003855.
STRINGi 9606.ENSP00000370223.

Chemistry

DrugBanki DB00157. NADH.

PTM databases

PhosphoSitei O43837.

Proteomic databases

MaxQBi O43837.
PaxDbi O43837.
PRIDEi O43837.

Protocols and materials databases

DNASUi 3420.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000380843 ; ENSP00000370223 ; ENSG00000101365 . [O43837-1 ]
ENST00000380851 ; ENSP00000370232 ; ENSG00000101365 . [O43837-2 ]
GeneIDi 3420.
KEGGi hsa:3420.
UCSCi uc002wgp.4. human. [O43837-1 ]
uc002wgq.4. human. [O43837-2 ]
uc002wgr.4. human. [O43837-3 ]

Organism-specific databases

CTDi 3420.
GeneCardsi GC20M002639.
GeneReviewsi IDH3B.
HGNCi HGNC:5385. IDH3B.
HPAi HPA049387.
HPA054180.
MIMi 604526. gene.
612572. phenotype.
neXtProti NX_O43837.
Orphaneti 791. Retinitis pigmentosa.
PharmGKBi PA29633.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG0473.
HOVERGENi HBG052080.
InParanoidi O43837.
KOi K00030.
OMAi ILATPDY.
OrthoDBi EOG75B85R.
PhylomeDBi O43837.
TreeFami TF315033.

Enzyme and pathway databases

BioCyci MetaCyc:ENSG00000101365-MONOMER.
Reactomei REACT_1785. Citric acid cycle (TCA cycle).
SABIO-RK O43837.

Miscellaneous databases

ChiTaRSi IDH3B. human.
GeneWikii IDH3B.
GenomeRNAii 3420.
NextBioi 13482.
PROi O43837.
SOURCEi Search...

Gene expression databases

ArrayExpressi O43837.
Bgeei O43837.
CleanExi HS_IDH3B.
Genevestigatori O43837.

Family and domain databases

Gene3Di 3.40.718.10. 1 hit.
InterProi IPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR004434. Isocitrate_DH_NAD.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view ]
PANTHERi PTHR11835. PTHR11835. 1 hit.
Pfami PF00180. Iso_dh. 1 hit.
[Graphical view ]
TIGRFAMsi TIGR00175. mito_nad_idh. 1 hit.
PROSITEi PS00470. IDH_IMDH. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Identification and functional characterization of a novel, tissue-specific NAD+-dependent isocitrate dehydrogenase beta subunit isoform."
    Kim Y.-O., Koh H.-J., Kim S.-H., Jo S.-H., Huh J.-W., Jeong K.-S., Lee I.J., Song B.J., Huh T.-L.
    J. Biol. Chem. 274:36866-36875(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS A AND B), VARIANT VAL-3, ALTERNATIVE SPLICING.
    Tissue: Heart.
  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 B AND C).
    Tissue: Placenta and Synovium.
  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 B).
    Tissue: Lung.
  6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 127-385 (ISOFORM B).
    Tissue: Uterus.
  7. "Lysine acetylation targets protein complexes and co-regulates major cellular functions."
    Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
    Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-199, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "Insights from retinitis pigmentosa into the roles of isocitrate dehydrogenases in the Krebs cycle."
    Hartong D.T., Dange M., McGee T.L., Berson E.L., Dryja T.P., Colman R.F.
    Nat. Genet. 40:1230-1234(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT RP46 PRO-132.

Entry informationi

Entry nameiIDH3B_HUMAN
AccessioniPrimary (citable) accession number: O43837
Secondary accession number(s): B2RDR1
, D3DVX2, D3DVX3, O95106, Q5JXS8, Q9NQ06, Q9NQ07, Q9NUZ0, Q9UEX0, Q9UG99
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: May 1, 2007
Last modified: September 3, 2014
This is version 150 of the entry and version 2 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

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. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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