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(-) Description

Title :  INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) COMPLEXED WITH 2,3-DIF GUANIDINO-NEU5AC2EN INHIBITOR
 
Authors :  V. A. Streltsov
Date :  25 Oct 12  (Deposition) - 01 May 13  (Release) - 01 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Neuraminidase, Sialidase, Hydrolase(O-Glucosyl), Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. -H. Kim, R. Resende, T. Wennekes, H. M. Chen, N. Bance, S. Buchini, A. G. Watts, P. Pilling, V. A. Streltsov, M. Petric, R. Liggins, S. Barrett, J. L. Mckimm-Breschkin, M. Niikura, S. G. Withers
Mechanism-Based Covalent Neuraminidase Inhibitors With Broad-Spectrum Influenza Antiviral Activity
Science V. 340 71 2013
PubMed-ID: 23429702  |  Reference-DOI: 10.1126/SCIENCE.1232552

(-) Compounds

Molecule 1 - NEURAMINIDASE
    Chains: A
    EC Number: 3.2.1.18
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 384509
    Strain: A/TERN/AUSTRALIA/G70C/1975(H11N9)
    Synonym: NEURAMINIDASE N9, SIALIDASE, HYDROLASE(O-GLYCOSYL)

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 21)

Asymmetric Unit (6, 21)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA1Ligand/IonCALCIUM ION
3GOL7Ligand/IonGLYCEROL
4MAN6Ligand/IonALPHA-D-MANNOSE
5NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
6ZGE1Ligand/Ion(2R,3R,4R)-3-ACETAMIDO-4-CARBAMIMIDAMIDO-5-FLUORANYL-2-[(1R,2R)-1,2,3-TRIS(OXIDANYL)PROPYL]-3,4-DIHYDRO-2H-PYRAN-6-CARBOXYLIC ACID
Biological Unit 1 (5, 80)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3GOL28Ligand/IonGLYCEROL
4MAN24Ligand/IonALPHA-D-MANNOSE
5NAG20Ligand/IonN-ACETYL-D-GLUCOSAMINE
6ZGE4Ligand/Ion(2R,3R,4R)-3-ACETAMIDO-4-CARBAMIMIDAMIDO-5-FLUORANYL-2-[(1R,2R)-1,2,3-TRIS(OXIDANYL)PROPYL]-3,4-DIHYDRO-2H-PYRAN-6-CARBOXYLIC ACID

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:146 , TRP A:437BINDING SITE FOR RESIDUE NAG A 512
02AC2SOFTWAREARG A:107 , HIS A:144 , ASN A:146 , GLY A:147 , SER A:153 , HOH A:635BINDING SITE FOR RESIDUE GOL A 513
03AC3SOFTWARECYS A:92 , ALA A:413 , GLU A:414 , CYS A:417 , ARG A:419 , HOH A:659 , HOH A:773 , HOH A:872 , HOH A:896 , HOH A:921BINDING SITE FOR RESIDUE GOL A 514
04AC4SOFTWARELYS A:102 , ASP A:103 , ASN A:104 , LEU A:115 , SER A:135 , GLY A:137 , TYR A:155 , ALA A:157 , SER A:164 , HOH A:762 , HOH A:869BINDING SITE FOR RESIDUE GOL A 515
05AC5SOFTWARELEU A:268 , ALA A:269 , GLY A:270 , ALA A:272 , HOH A:717BINDING SITE FOR RESIDUE GOL A 516
06AC6SOFTWARESER A:367 , ALA A:369 , SER A:370 , ASN A:400 , HOH A:959BINDING SITE FOR RESIDUE GOL A 517
07AC7SOFTWARELYS A:336 , CYS A:337 , ASN A:338 , ASP A:339 , HOH A:889BINDING SITE FOR RESIDUE GOL A 518
08AC8SOFTWAREHIS A:150 , ASP A:151 , ARG A:152 , HOH A:625 , HOH A:960BINDING SITE FOR RESIDUE GOL A 519
09AC9SOFTWAREARG A:118 , GLU A:119 , ASP A:151 , ARG A:152 , ARG A:156 , TRP A:178 , ILE A:222 , ARG A:224 , GLU A:227 , ALA A:246 , GLU A:276 , GLU A:277 , ARG A:292 , ARG A:371 , TYR A:406 , HOH A:684 , HOH A:701 , HOH A:751 , HOH A:757 , HOH A:865 , HOH A:938BINDING SITE FOR RESIDUE ZGE A 520
10BC1SOFTWAREASP A:293 , GLY A:297 , ASP A:324 , ASN A:347 , HOH A:763 , HOH A:832BINDING SITE FOR RESIDUE CA A 521
11BC2SOFTWAREASN A:200 , ARG A:327 , ASN A:329 , ASP A:330 , ARG A:364 , ILE A:366 , ILE A:368 , GLU A:375 , LEU A:377 , LYS A:389 , PRO A:390 , THR A:391 , GLN A:392 , GLY A:394 , LEU A:453 , GLY A:454 , GLN A:455 , HOH A:646 , HOH A:687 , HOH A:735 , HOH A:736 , HOH A:782 , HOH A:819 , HOH A:820 , HOH A:824 , HOH A:875 , HOH A:876 , HOH A:905 , HOH A:916 , HOH A:917 , HOH A:918 , HOH A:919 , HOH A:980BINDING SITE FOR LINKED RESIDUES A 501 to 509
12BC3SOFTWAREASP A:83 , PHE A:84 , ASN A:86 , ASN A:234 , HOH A:704 , HOH A:954BINDING SITE FOR LINKED RESIDUES A 510 to 511

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:92 -A:417
2A:124 -A:129
3A:175 -A:193
4A:183 -A:230
5A:232 -A:237
6A:278 -A:291
7A:280 -A:289
8A:318 -A:337
9A:421 -A:447

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:325 -Pro A:326
2Arg A:430 -Pro A:431

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W09)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W09)

(-) Exons   (0, 0)

(no "Exon" information available for 3W09)

(-) 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 d3w09a_ A: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhhh....eeeeeeeeeee..eeeeeeeeeeee..hhhhh..........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee....................eeeeeeee.....eeeeeeeee..eeeeeee........eeeeeeee..eeeeeee........eeeeee....eeeeee...................................ee......eeee.......eeeeeee.............eeeeeeeeeee...eeeee..........eeeeeeeeee.........eeeeeeeeeee.............hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3w09 A   82 RDFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRALISWPLSSPPTVYNSRVECIGWSSTSCHDGKTRMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESECVCHNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLAGTAKHIEECSCYGERAEITCTCRDNWQGSNRPVIRIDPVAMTHTSQYICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGVNTWLGRTISIASRSGYEMLKVPNALTDDKSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWDWPDGAKIEYFL  468
                                    91       101       111       121       131       141       151       161       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330  ||   341       351       361       371       381       391||     402       412||     420       430       440       450       460        
                                                                                                                 169A                                                                                                                                                                 333|                                                      392|               412A|                                                        
                                                                                                                                                                                                                                                                                       335                                                       394                412B
   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  (0, 0)

(no "CATH Domain" information available for 3W09)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W09)

(-) 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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  3w09
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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 1iny 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 4dgr 4nn9 4weg 5nn9 6nn9 7nn9

(-) Related Entries Specified in the PDB File

1nnc 7nn9