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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN SIALIDASE NEU2 IN COMPLEX WITH 2',3'- DIHYDROXYPROPYL ETHER MIMETIC INHIBITOR
 
Authors :  L. M. G. Chavas, R. Kato, M. C. Mann, R. J. Thomson, J. C. Dyason, M. Von Itzstein, P. Fusi, C. Tringali, B. Venerando, G. Tettamanti, E. Monti S. Wakatsuki
Date :  14 Nov 05  (Deposition) - 21 Nov 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym./Biol. Unit :  A
Keywords :  Sialidase, Neuraminidase, Influenza Virus, Drug Design, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. M. G. Chavas, R. Kato, M. C. Mann, R. J. Thomson, J. C. Dyason, M. Von Itzstein, P. Fusi, C. Tringali, B. Venerando, G. Tettamanti, E. Monti, S. Wakatsuki
Crystal Structure Of The Human Sialidase Neu2 In Complex With 2', 3'- Dihydroxypropyl Ether Mimetic Inhibitor
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIALIDASE 2
    ChainsA
    EC Number3.2.1.18
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-2T
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNEU2, CYTOSOLIC SIALIDASE, N-ACETYL-ALPHA- NEURAMINIDASE 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1DYM1Ligand/Ion6-(2,3-DIHYDROXYPROPOXY)-5-ACETAMIDO-5,6-DIHYDRO-4-HYDROXY-4H-PYRAN-2-CARBOXYLIC ACID
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:16 , ALA A:17 , HIS A:18 , TYR A:20 , PRO A:316 , HOH A:1059BINDING SITE FOR RESIDUE PO4 A 1002
2AC2SOFTWAREARG A:21 , ILE A:22 , ARG A:41 , MET A:85 , TYR A:179 , TYR A:181 , LEU A:217 , GLU A:218 , ARG A:237 , ARG A:304 , TYR A:334 , HOH A:1060 , HOH A:1130BINDING SITE FOR RESIDUE DYM A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F13)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:160 -Pro A:161
2Pro A:315 -Pro A:316

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024461S11RNEUR2_HUMANPolymorphism2233384AS11R
2UniProtVAR_024462R41QNEUR2_HUMANPolymorphism2233385AR41Q
3UniProtVAR_049204A145TNEUR2_HUMANPolymorphism2233390AA145T
4UniProtVAR_055311H168NNEUR2_HUMANPolymorphism2233391AN168N
5UniProtVAR_055312R182QNEUR2_HUMANPolymorphism2233393AR182Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F13)

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002338401ENSE00001709784chr2:233897382-233897582201NEUR2_HUMAN1-67671A:3-67 (gaps)65
1.2ENST000002338402ENSE00000786879chr2:233898826-233899767942NEUR2_HUMAN68-3803131A:68-376 (gaps)309

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:351
 aligned with NEUR2_HUMAN | Q9Y3R4 from UniProtKB/Swiss-Prot  Length:380

    Alignment length:374
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372    
          NEUR2_HUMAN     3 SLPVLQKESVFQSGAHAYRIPALLYLPGQQSLLAFAEQRASKKDEHAELIVLRRGDYDAPTHQVQWQAQEVVAQARLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQVTEQQQLQTRANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLHDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVETGEQRVVTLNARSHLRARVQAQSTNDGLDFQESQLVKKLVEPPPQGCQGSVISFPSPRSGPGSPAQWLLYTHPTHSWQRADLGAYLNPRPPAPEAWSEPVLLAKGSCAYSDLQSMGTGPDGSPLFGCLYEANDYEEIVFLMFTLKQAFPAE 376
               SCOP domains d2f13a_ A: Sialidase 2 (Neu2)                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee....eeeeeeeeeehhh.eeeeeeeee.------..eeeeeeeeee....eeee...ee........eeeeeeeeeee....eeeeeeeeee..---------.....eeeeeee..........eehhhhhhhhhhh.eeeeee.....ee.......eeeeeeeee........eeeeeeeee.......ee.......eeeeeeeee.--...eeeeeeee...eeeeeee........eeeeeeeee.........eeeeee...------.eeeeeeee......eeeeeeee....hhhhh...eeeeeeeeeeeeeeeeee.....eeeeeeeee....eeeeeeeehhhhh... Sec.struct. author
                 SAPs(SNPs) --------R-----------------------------Q-------------------------------------------------------------------------------------------------------T----------------------N-------------Q-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-67 (gaps) UniProt: 1-67 [INCOMPLETE]          Exon 1.2  PDB: A:68-376 (gaps) UniProt: 68-380 [INCOMPLETE]                                                                                                                                                                                                                                                           Transcript 1
                 2f13 A   3 SLPVLQKESVFQSGAHAYRIPALLYLPGQQSLLAFAEQRA------AELIVLRRGDYDAPTHQVQWQAQEVVAQARLDGHRSMNPCPLYDAQTGTLFLFFIAIPGQ---------RANVTRLCQVTSTDHGRTWSSPRDLTDAAIGPAYREWSTFAVGPGHCLQLNDRARSLVVPAYAYRKLHPIQRPIPSAFCFLSHDHGRTWARGHFVAQDTLECQVAEVE--EQRVVTLNARSHLRARVQAQSTNDGLDFQESQLVKKLVEPPPQGCQGSVISFPSPR------AQWLLYTHPTHSWQRADLGAYLNPRPPAPEAWSEPVLLAKGSCAYSDLQSMGTGPDGSPLFGCLYEANDYEEIVFLMFTLKQAFPAE 376
                                    12        22        32        42      | 52        62        72        82        92       102     |   -     | 122       132       142       152       162       172       182       192       202       212       222  |  | 232       242       252       262       272       282|      292       302       312       322       332       342       352       362       372    
                                                                  42     49                                                        108       118                                                                                                        225  |                                                    283    290                                                                                      
                                                                                                                                                                                                                                                           228                                                                                                                                                    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2F13)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F13)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NEUR2_HUMAN | Q9Y3R4)
molecular function
    GO:0052794    exo-alpha-(2->3)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->3)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0052795    exo-alpha-(2->6)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->6)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0052796    exo-alpha-(2->8)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->8)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0004308    exo-alpha-sialidase activity    Catalysis of the hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006689    ganglioside catabolic process    The chemical reactions and pathways resulting in the breakdown of ganglioside, a ceramide oligosaccharide carrying, in addition to other sugar residues, one or more sialic residues.
    GO:0006687    glycosphingolipid metabolic process    The chemical reactions and pathways involving glycosphingolipids, any compound with residues of sphingoid and at least one monosaccharide.
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0009313    oligosaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.
    GO:0045663    positive regulation of myoblast differentiation    Any process that activates or increases the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
    GO:0010831    positive regulation of myotube differentiation    Any process that activates, maintains or increases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
    GO:0045471    response to ethanol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NEUR2_HUMAN | Q9Y3R41snt 1so7 1vcu 2f0z 2f10 2f11 2f12 2f24 2f25 2f26 2f27 2f28 2f29 4nc5 4ncs

(-) Related Entries Specified in the PDB File

1snt HUMAN NEU2 APO-FORM
1so7 HUMAN NEU2 SUGAR-INDUCED FORM
1vcu HUMAN NEU2-DANA COMPLEX
2f0z
2f10
2f11
2f12
2f24
2f25
2f26
2f27
2f28
2f29