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(-) Description

Title :  INFLUENZA NA IN COMPLEX WITH ANTIVIRAL COMPOUND
 
Authors :  P. S. Kerry, R. J. M. R. Russell
Date :  11 Jan 12  (Deposition) - 13 Feb 13  (Release) - 13 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Hydrolase, Neuraminidase, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Bhatt, R. Bohm, P. S. Kerry, J. C. Dyason, R. J. Russell, R. J. Thomson M. Von Itzstein
Exploring The Interactions Of Unsaturated Glucuronides With Influenza Virus Sialidase.
J. Med. Chem. V. 55 8963 2012
PubMed-ID: 23017008  |  Reference-DOI: 10.1021/JM301145K

(-) Compounds

Molecule 1 - NEURAMINIDASE
    Chains: A
    EC Number: 3.2.1.18
    Mutation: YES
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 385580
    Strain: A/DUCK/UKRAINE/1/1963 H3N8

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
10HX1Ligand/IonPENTAN-3-YL 2-(ACETYLAMINO)-2,4-DIDEOXY-ALPHA-L-THREO-HEX-4-ENOPYRANOSIDURONIC ACID
2CA1Ligand/IonCALCIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
10HX4Ligand/IonPENTAN-3-YL 2-(ACETYLAMINO)-2,4-DIDEOXY-ALPHA-L-THREO-HEX-4-ENOPYRANOSIDURONIC ACID
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:293 , GLY A:297 , ASP A:324 , TYR A:347 , GLY A:348 , HOH A:620BINDING SITE FOR RESIDUE CA A 501
2AC2SOFTWAREARG A:118 , GLU A:119 , ASP A:151 , ARG A:152 , TRP A:178 , GLU A:276 , GLU A:277 , ARG A:292 , ASN A:294 , ARG A:371 , TYR A:406 , HOH A:675BINDING SITE FOR RESIDUE 0HX A 502

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:92 -A:417
2A:124 -A:129
3A:183 -A:230
4A:232 -A:237
5A:278 -A:291
6A:280 -A:289
7A:318 -A:337
8A:421 -A:447

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Thr A:325 -Pro A:326
2Lys A:430 -Pro A:431
3Leu A:464 -Pro A:465

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D8S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D8S)

(-) Exons   (0, 0)

(no "Exon" information available for 4D8S)

(-) Sequences/Alignments

Asymmetric 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:388
 aligned with NRAM_I63A3 | Q07599 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:388
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460        
          NRAM_I63A3     81 TYMNNTEAICDAKGFAPFSKDNGIRIGSRGHIFVIREPFVSCSPIECRTFFLTQGSLLNDKHSNGTVKDRSPFRTLMSVEVGQSPNVYQARFEAVAWSATACHDGKKWMTVGVTGPDSKAVAVIHYGGVPTDVVNSWAGDILRTQESSCTCIQGDCYWVMTDGPANRQAQYRIYKANQGRIIGQTDISFNGGHIEECSCYPNDGKVECVCRDGWTGTNRPVLVISPDLSYRVGYLCAGIPSDTPRGEDTQFTGSCTSPMGNQGYGVKGFGFRQGTDVWMGRTISRTSRSGFEILRIKNGWTQTSKEQIRKQVVVDNLNWSGYSGSFTLPVELSGKDCLVPCFWVEMIRGKPEEKTIWTSSSSIVMCGVDYEVADWSWHDGAILPFDID  468
               SCOP domains d4d8sa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee.hhhhhhh....eeeeeeeeee....eeeeeeeeeee..hhhhh..........eeeeee.....hhhhheeeee..eeeeee....eeeeeee......eeeeee..eeeeeee..............eee..eeeeeeee.......eeeeeeee..eeeeeeee.......eeeeeeee..eeeeeee........eeeee.....eeeee...................................eeee..eeeeee.......eeeeeeee..........eeeeeeeeeeeee...eeeeeehhhhhh....eeeeeeeeeee........eeeeeeeeeee.................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4d8s A   83 TYMNNTEAICDAKGFAPFSKDNGIRIGSRGHIFVIREPFVSCSPIECRTFFLTQGSLLNDKHSNGTVKDRSPFRTLMSVEVGQSPNVYQARFEAVAWSATACHDGKKWMTVGVTGPDSKAVAVIHYGGVPTDVVNSWAGDILRTQESSCTCIQGDCYWVMTDGPANRQAQYRIYKANQGRIIGQTDISFNGGHIEECSCYPNDGKVECVCRDNWTGTNRPVLVISPDLSYRVGYLCAGIPSDTPRGEDTQFTGSCTSPMGNQGYGVKGFGFRQGTDVWMGRTISRTSRSGFEILRIKNGWTQTSKEQIRKQVVVDNLNWSGYSGSFTLPVELSGKDCLVPCFWVEMIRGKPEEKTIWTSSSSIVMCGVDYEVADWSWHDGAILPFDID  469
                                    92       102       112       122       132       142       152       162       171       181       191       201       211       221       231       241       251       261       271       281       291       301    || 312       322      330B|||    342|      353       363       373       383       394       404      412B||     420       430  ||   441       451       461        
                                                                                                                169A                                                                                                                                      306|                   330A||||    342|                                             392|               412A|||                  433|                                  
                                                                                                                                                                                                                                                           308                    330B|||     344                                              394                412B||                   435                                  
                                                                                                                                                                                                                                                                                    332||                                                                          412C|                                                        
                                                                                                                                                                                                                                                                                     333|                                                                           412D                                                        
                                                                                                                                                                                                                                                                                      335
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D8S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D8S)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (NRAM_I63A3 | Q07599)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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: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.
cellular component
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NRAM_I63A3 | Q07599: 2ht5 2ht7 2ht8 2htq 2htr 2htu 3o9j 3o9k 4gb1 4ks1 4m3m 4mju 4mjv

(-) Related Entries Specified in the PDB File

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