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Q9NVS9

- PNPO_HUMAN

UniProt

Q9NVS9 - PNPO_HUMAN

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Protein

Pyridoxine-5'-phosphate oxidase

Gene

PNPO

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).1 Publication

Catalytic activityi

Pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + H2O2.
Pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2.

Cofactori

Binds 1 FMN per subunit.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei95 – 951FMN1 Publication
Binding sitei98 – 981FMN; via amide nitrogen1 Publication
Binding sitei100 – 1001Substrate
Binding sitei117 – 1171FMN1 Publication
Binding sitei157 – 1571Substrate
Binding sitei161 – 1611Substrate
Binding sitei165 – 1651Substrate

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi110 – 1112FMN1 Publication
Nucleotide bindingi174 – 1752FMN1 Publication

GO - Molecular functioni

  1. FMN binding Source: InterPro
  2. pyridoxamine-phosphate oxidase activity Source: Reactome

GO - Biological processi

  1. pyridoxine biosynthetic process Source: UniProtKB-KW
  2. small molecule metabolic process Source: Reactome
  3. vitamin B6 metabolic process Source: Reactome
  4. vitamin metabolic process Source: Reactome
  5. water-soluble vitamin metabolic process Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Pyridoxine biosynthesis

Keywords - Ligandi

Flavoprotein, FMN, Pyridoxal phosphate

Enzyme and pathway databases

BioCyciMetaCyc:HS03105-MONOMER.
ReactomeiREACT_25012. Vitamins B6 activation to pyridoxal phosphate.
SABIO-RKQ9NVS9.
UniPathwayiUPA00190; UER00304.
UPA00190; UER00305.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxine-5'-phosphate oxidase (EC:1.4.3.5)
Alternative name(s):
Pyridoxamine-phosphate oxidase
Gene namesi
Name:PNPO
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 17

Organism-specific databases

HGNCiHGNC:30260. PNPO.

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: Reactome
  2. extracellular vesicular exosome Source: UniProt
Complete GO annotation...

Pathology & Biotechi

Involvement in diseasei

Pyridoxine-5'-phosphate oxidase deficiency (PNPO deficiency) [MIM:610090]: The main feature of neonatal epileptic encephalopathy is the onset within hours of birth of a severe seizure disorder that does not respond to anticonvulsant drugs and can be fatal. Seizures can cease with the administration of PLP, being resistant to treatment with pyridoxine,.1 Publication
Note: The disease is caused by mutations affecting the gene represented in this entry.
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti229 – 2291R → W in PNPO deficiency; strong activity decrease. 1 Publication
Corresponds to variant rs104894629 [ dbSNP | Ensembl ].
VAR_029360

Keywords - Diseasei

Disease mutation, Epilepsy

Organism-specific databases

MIMi610090. phenotype.
Orphaneti79096. Pyridoxal phosphate-responsive seizures.
PharmGKBiPA134915565.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 261261Pyridoxine-5'-phosphate oxidasePRO_0000167783Add
BLAST

Proteomic databases

MaxQBiQ9NVS9.
PaxDbiQ9NVS9.
PeptideAtlasiQ9NVS9.
PRIDEiQ9NVS9.

2D gel databases

REPRODUCTION-2DPAGEIPI00018272.

PTM databases

PhosphoSiteiQ9NVS9.

Expressioni

Gene expression databases

BgeeiQ9NVS9.
CleanExiHS_PNPO.
ExpressionAtlasiQ9NVS9. baseline and differential.
GenevestigatoriQ9NVS9.

Organism-specific databases

HPAiHPA023204.
HPA027776.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi120463. 8 interactions.
STRINGi9606.ENSP00000225573.

Structurei

Secondary structure

1
261
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi58 – 7114
Beta strandi80 – 867
Beta strandi88 – 903
Beta strandi92 – 987
Beta strandi102 – 1054
Beta strandi106 – 1127
Helixi116 – 1238
Beta strandi126 – 1338
Helixi134 – 1363
Beta strandi138 – 14811
Helixi151 – 16010
Helixi163 – 1719
Helixi181 – 19414
Turni195 – 1973
Beta strandi206 – 2116
Beta strandi214 – 2207
Beta strandi228 – 2347
Beta strandi254 – 2585

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NRGX-ray1.95A1-261[»]
3HY8X-ray2.50A1-261[»]
DisProtiDP00168.
ProteinModelPortaliQ9NVS9.
SMRiQ9NVS9. Positions 49-261.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9NVS9.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni225 – 2273Substrate binding

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0259.
GeneTreeiENSGT00390000011219.
HOGENOMiHOG000242755.
HOVERGENiHBG045634.
KOiK00275.
OMAiNMGSRKA.
PhylomeDBiQ9NVS9.
TreeFamiTF313411.

Family and domain databases

Gene3Di2.30.110.10. 1 hit.
HAMAPiMF_01629. PdxH.
InterProiIPR000659. Pyridox_Oxase.
IPR019740. Pyridox_Oxase_CS.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
[Graphical view]
PANTHERiPTHR10851. PTHR10851. 1 hit.
PfamiPF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
[Graphical view]
PIRSFiPIRSF000190. Pyd_amn-ph_oxd. 1 hit.
SUPFAMiSSF50475. SSF50475. 1 hit.
TIGRFAMsiTIGR00558. pdxH. 1 hit.
PROSITEiPS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q9NVS9-1) [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

        10         20         30         40         50
MTCWLRGVTA TFGRPAEWPG YLSHLCGRSA AMDLGPMRKS YRGDREAFEE
60 70 80 90 100
THLTSLDPVK QFAAWFEEAV QCPDIGEANA MCLATCTRDG KPSARMLLLK
110 120 130 140 150
GFGKDGFRFF TNFESRKGKE LDSNPFASLV FYWEPLNRQV RVEGPVKKLP
160 170 180 190 200
EEEAECYFHS RPKSSQIGAV VSHQSSVIPD REYLRKKNEE LEQLYQDQEV
210 220 230 240 250
PKPKSWGGYV LYPQVMEFWQ GQTNRLHDRI VFRRGLPTGD SPLGPMTHRG
260
EEDWLYERLA P
Length:261
Mass (Da):29,988
Last modified:October 1, 2000 - v1
Checksum:i2C74E9F962FE2A95
GO
Isoform 2 (identifier: Q9NVS9-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-95: Missing.

Note: No experimental confirmation available.

Show »
Length:166
Mass (Da):19,478
Checksum:i81A7843218C16A1D
GO
Isoform 3 (identifier: Q9NVS9-3) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     122-139: Missing.

Note: No experimental confirmation available.

Show »
Length:243
Mass (Da):27,823
Checksum:i0E1F950A074A37D7
GO
Isoform 4 (identifier: Q9NVS9-4) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     140-182: Missing.

Note: No experimental confirmation available.

Show »
Length:218
Mass (Da):25,200
Checksum:i710BED8B9D98115F
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti50 – 501E → K.1 Publication
VAR_029358
Natural varianti116 – 1161R → Q.
Corresponds to variant rs17679445 [ dbSNP | Ensembl ].
VAR_029359
Natural varianti229 – 2291R → W in PNPO deficiency; strong activity decrease. 1 Publication
Corresponds to variant rs104894629 [ dbSNP | Ensembl ].
VAR_029360

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 9595Missing in isoform 2. 1 PublicationVSP_056409Add
BLAST
Alternative sequencei122 – 13918Missing in isoform 3. 1 PublicationVSP_056410Add
BLAST
Alternative sequencei140 – 18243Missing in isoform 4. 1 PublicationVSP_056411Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF468030 mRNA. Translation: AAM76918.1.
AK001397 mRNA. Translation: BAA91668.1.
AK303536 mRNA. Translation: BAG64562.1.
AK303665 mRNA. Translation: BAG64664.1.
AK303792 mRNA. Translation: BAG64749.1.
CH471109 Genomic DNA. Translation: EAW94770.1.
CH471109 Genomic DNA. Translation: EAW94771.1.
BC006525 mRNA. Translation: AAH06525.1.
CCDSiCCDS11522.1. [Q9NVS9-1]
RefSeqiNP_060599.1. NM_018129.3.
UniGeneiHs.631742.

Genome annotation databases

EnsembliENST00000225573; ENSP00000225573; ENSG00000108439. [Q9NVS9-1]
ENST00000434554; ENSP00000399960; ENSG00000108439. [Q9NVS9-4]
GeneIDi55163.
KEGGihsa:55163.
UCSCiuc002imo.3. human. [Q9NVS9-1]

Polymorphism databases

DMDMi37082126.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF468030 mRNA. Translation: AAM76918.1 .
AK001397 mRNA. Translation: BAA91668.1 .
AK303536 mRNA. Translation: BAG64562.1 .
AK303665 mRNA. Translation: BAG64664.1 .
AK303792 mRNA. Translation: BAG64749.1 .
CH471109 Genomic DNA. Translation: EAW94770.1 .
CH471109 Genomic DNA. Translation: EAW94771.1 .
BC006525 mRNA. Translation: AAH06525.1 .
CCDSi CCDS11522.1. [Q9NVS9-1 ]
RefSeqi NP_060599.1. NM_018129.3.
UniGenei Hs.631742.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1NRG X-ray 1.95 A 1-261 [» ]
3HY8 X-ray 2.50 A 1-261 [» ]
DisProti DP00168.
ProteinModelPortali Q9NVS9.
SMRi Q9NVS9. Positions 49-261.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 120463. 8 interactions.
STRINGi 9606.ENSP00000225573.

PTM databases

PhosphoSitei Q9NVS9.

Polymorphism databases

DMDMi 37082126.

2D gel databases

REPRODUCTION-2DPAGE IPI00018272.

Proteomic databases

MaxQBi Q9NVS9.
PaxDbi Q9NVS9.
PeptideAtlasi Q9NVS9.
PRIDEi Q9NVS9.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000225573 ; ENSP00000225573 ; ENSG00000108439 . [Q9NVS9-1 ]
ENST00000434554 ; ENSP00000399960 ; ENSG00000108439 . [Q9NVS9-4 ]
GeneIDi 55163.
KEGGi hsa:55163.
UCSCi uc002imo.3. human. [Q9NVS9-1 ]

Organism-specific databases

CTDi 55163.
GeneCardsi GC17P046018.
HGNCi HGNC:30260. PNPO.
HPAi HPA023204.
HPA027776.
MIMi 603287. gene.
610090. phenotype.
neXtProti NX_Q9NVS9.
Orphaneti 79096. Pyridoxal phosphate-responsive seizures.
PharmGKBi PA134915565.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG0259.
GeneTreei ENSGT00390000011219.
HOGENOMi HOG000242755.
HOVERGENi HBG045634.
KOi K00275.
OMAi NMGSRKA.
PhylomeDBi Q9NVS9.
TreeFami TF313411.

Enzyme and pathway databases

UniPathwayi UPA00190 ; UER00304 .
UPA00190 ; UER00305 .
BioCyci MetaCyc:HS03105-MONOMER.
Reactomei REACT_25012. Vitamins B6 activation to pyridoxal phosphate.
SABIO-RK Q9NVS9.

Miscellaneous databases

ChiTaRSi PNPO. human.
EvolutionaryTracei Q9NVS9.
GeneWikii PNPO.
GenomeRNAii 55163.
NextBioi 35476859.
PROi Q9NVS9.
SOURCEi Search...

Gene expression databases

Bgeei Q9NVS9.
CleanExi HS_PNPO.
ExpressionAtlasi Q9NVS9. baseline and differential.
Genevestigatori Q9NVS9.

Family and domain databases

Gene3Di 2.30.110.10. 1 hit.
HAMAPi MF_01629. PdxH.
InterProi IPR000659. Pyridox_Oxase.
IPR019740. Pyridox_Oxase_CS.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
[Graphical view ]
PANTHERi PTHR10851. PTHR10851. 1 hit.
Pfami PF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
[Graphical view ]
PIRSFi PIRSF000190. Pyd_amn-ph_oxd. 1 hit.
SUPFAMi SSF50475. SSF50475. 1 hit.
TIGRFAMsi TIGR00558. pdxH. 1 hit.
PROSITEi PS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. Kwon O.-S.
    Submitted (JAN-2002) to the EMBL/GenBank/DDBJ databases
    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; 3 AND 4).
    Tissue: Liver, Teratocarcinoma, Thymus and Thyroid.
  3. "DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage."
    Zody M.C., Garber M., Adams D.J., Sharpe T., Harrow J., Lupski J.R., Nicholson C., Searle S.M., Wilming L., Young S.K., Abouelleil A., Allen N.R., Bi W., Bloom T., Borowsky M.L., Bugalter B.E., Butler J., Chang J.L.
    , Chen C.-K., Cook A., Corum B., Cuomo C.A., de Jong P.J., DeCaprio D., Dewar K., FitzGerald M., Gilbert J., Gibson R., Gnerre S., Goldstein S., Grafham D.V., Grocock R., Hafez N., Hagopian D.S., Hart E., Norman C.H., Humphray S., Jaffe D.B., Jones M., Kamal M., Khodiyar V.K., LaButti K., Laird G., Lehoczky J., Liu X., Lokyitsang T., Loveland J., Lui A., Macdonald P., Major J.E., Matthews L., Mauceli E., McCarroll S.A., Mihalev A.H., Mudge J., Nguyen C., Nicol R., O'Leary S.B., Osoegawa K., Schwartz D.C., Shaw-Smith C., Stankiewicz P., Steward C., Swarbreck D., Venkataraman V., Whittaker C.A., Yang X., Zimmer A.R., Bradley A., Hubbard T., Birren B.W., Rogers J., Lander E.S., Nusbaum C.
    Nature 440:1045-1049(2006) [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: Lymph.
  6. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  7. "Structure and properties of recombinant human pyridoxine 5'-phosphate oxidase."
    Musayev F.N., Di Salvo M.L., Ko T.-P., Schirch V., Safo M.K.
    Protein Sci. 12:1455-1463(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 49-161 IN COMPLEX WITH FMN AND PYRIDOXAL 5'-PHOSPHATE, PARTIAL PROTEIN SEQUENCE, SUBUNIT, ENZYME REGULATION, FUNCTION.
  8. "Neonatal epileptic encephalopathy caused by mutations in the PNPO gene encoding pyridox(am)ine 5'-phosphate oxidase."
    Mills P.B., Surtees R.A.H., Champion M.P., Beesley C.E., Dalton N., Scambler P.J., Heales S.J.R., Briddon A., Scheimberg I., Hoffmann G.F., Zschocke J., Clayton P.T.
    Hum. Mol. Genet. 14:1077-1086(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT PNPO DEFICIENCY TRP-229, VARIANT LYS-50.

Entry informationi

Entry nameiPNPO_HUMAN
AccessioniPrimary (citable) accession number: Q9NVS9
Secondary accession number(s): B4E0V0
, B4E152, B4E1D7, D3DTT9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 26, 2003
Last sequence update: October 1, 2000
Last modified: October 29, 2014
This is version 133 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, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 17
    Human chromosome 17: 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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  7. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3