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(-) Description

Title :  A SIALIC ACID DERIVED PHOSPHONATE ANALOG INHIBITS DIFFERENT STRAINS OF INFLUENZA VIRUS NEURAMINIDASE WITH DIFFERENT EFFICIENCIES
 
Authors :  C. L. White, M. N. Janakiraman, W. G. Laver, C. Philippon, A. Vasella, G. M. Luo
Date :  26 Sep 94  (Deposition) - 07 Feb 95  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Hydrolase, O-Glycosyl, Neuraminidase, Sialidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. L. White, M. N. Janakiraman, W. G. Laver, C. Philippon, A. Vasella, G. M. Air, M. Luo
A Sialic Acid-Derived Phosphonate Analog Inhibits Different Strains Of Influenza Virus Neuraminidase With Different Efficiencies.
J. Mol. Biol. V. 245 623 1995
PubMed-ID: 7844831  |  Reference-DOI: 10.1006/JMBI.1994.0051
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INFLUENZA A SUBTYPE N9 NEURAMINIDASE
    Chains: A
    EC Number: 3.2.1.18
    Engineered: YES
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric Unit (5, 11)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA1Ligand/IonCALCIUM ION
3EQP1Ligand/Ion(4-ACETAMIDO-2,4-DIDEOXY-D-GLYCERO-ALPHA-D-GALACTO-1-OCTOPYRANOSYL)PHOSPHONIC ACID
4MAN4Ligand/IonALPHA-D-MANNOSE
5NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 40)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3EQP4Ligand/Ion(4-ACETAMIDO-2,4-DIDEOXY-D-GLYCERO-ALPHA-D-GALACTO-1-OCTOPYRANOSYL)PHOSPHONIC ACID
4MAN16Ligand/IonALPHA-D-MANNOSE
5NAG16Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:83 , PHE A:84 , ASN A:86BINDING SITE FOR RESIDUE NAG A 470A
02AC2SOFTWAREASN A:146 , TRP A:438BINDING SITE FOR RESIDUE NAG A 471A
03AC3SOFTWAREASN A:200 , ASN A:201 , ARG A:221 , GLY A:455 , GLN A:456 , NAG A:473BBINDING SITE FOR RESIDUE NAG A 472A
04AC4SOFTWAREGLY A:393 , NAG A:472A , BMA A:474CBINDING SITE FOR RESIDUE NAG A 473B
05AC5SOFTWAREPRO A:390 , THR A:391 , GLY A:393 , NAG A:473B , MAN A:475D , MAN A:478GBINDING SITE FOR RESIDUE BMA A 474C
06AC6SOFTWAREARG A:364 , GLU A:375 , BMA A:474C , MAN A:476EBINDING SITE FOR RESIDUE MAN A 475D
07AC7SOFTWAREASP A:331 , LYS A:389 , PRO A:390 , MAN A:475D , MAN A:477FBINDING SITE FOR RESIDUE MAN A 476E
08AC8SOFTWAREARG A:328 , ASN A:330 , ASP A:331 , ILE A:366 , ILE A:368 , MAN A:476E , HOH A:548BINDING SITE FOR RESIDUE MAN A 477F
09AC9SOFTWARETHR A:391 , BMA A:474CBINDING SITE FOR RESIDUE MAN A 478G
10BC1SOFTWAREASP A:294 , GLY A:298 , ASP A:325 , ASN A:347 , HOH A:503BINDING SITE FOR RESIDUE CA A 479
11BC2SOFTWAREARG A:118 , GLU A:119 , ASP A:151 , ARG A:152 , ALA A:247 , GLU A:277 , ARG A:293 , ARG A:371 , TYR A:405 , HOH A:531 , HOH A:533 , HOH A:551BINDING SITE FOR RESIDUE EQP A 500
12CATAUTHORARG A:118 , GLU A:119 , ASP A:151 , ARG A:152 , TRP A:179 , ILE A:223 , ARG A:225 , GLU A:277 , ARG A:293 , ARG A:371 , TYR A:405SUBSTRATE (SIALIC ACID) BINDING RESIDUES IN CATALYTIC SITE

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:92 -A:418
2A:124 -A:129
3A:176 -A:194
4A:184 -A:231
5A:233 -A:238
6A:279 -A:292
7A:281 -A:290
8A:319 -A:337
9A:422 -A:448

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:326 -Pro A:327
2Arg A:431 -Pro A:432

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1INY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1INY)

(-) Exons   (0, 0)

(no "Exon" information available for 1INY)

(-) 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_I75A5 | P03472 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:388
                                    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       382       392       402       412       422       432       442       452       462        
           NRAM_I75A5    83 RDFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRALISWPLSSPPTVYNSRVECIGWSSTSCHDGKTRMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESECVCHNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLAGTAKHIEECSCYGERAEITCTCRDNWQGSNRPVIRIDPVAMTHTSQYICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGVNTWLGRTISIASRSGYEMLKVPNALTDDKSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWDWPDGAKIEYFL 470
               SCOP domains d1inya_ A: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1inyA00 A:82-469  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee....eeeeeee.hhhhhhhhh..eeeeeeeeee....eeeeeeeeeee..hhhhh..........eeeeee..........eeeee...eeeee....eeeeeee......eeeeee..eeeeeee...................eeeeeeee.......eeeeeeee..eeeeeee...........eeeee..eeeee..........eeeeee....eeeeee...................................ee......eeee.......eeeeeee.............eeeeeeeeeee...eeeee.......ee.eeeeeeeeee.........eeeeeeeeeee.............hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iny A  82 RDFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRALISWPLSSPPTVYNSRVECIGWSSTSCHDGKTRMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESECVCHNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLAGTAKHIEECSCYGERAEITCTCRDNWQGSNRPVIRIDPVAMTHTSQYICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGVNTWLGRTISIALRSGYEMLKVPNALTDDKSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWDWPDGAKIEYFL 469
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1INY)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (NRAM_I75A5 | P03472)
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_I75A5 | P03472: 1a14 1bji 1f8b 1f8c 1f8d 1f8e 1l7f 1l7g 1l7h 1mwe 1nca 1ncb 1ncc 1nmc 1nna 1nnb 1nnc 1xoe 1xog 2c4a 2c4l 2qwa 2qwb 2qwc 2qwd 2qwe 2qwf 2qwg 2qwh 2qwi 2qwj 2qwk 3nn9 3w09 4dgr 4nn9 4weg 5nn9 6nn9 7nn9

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