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(-) Description

Title :  THE X-RAY STRUCTURE OF A COMPLEX OF 4-AMINO-NEU5AC2EN AND A DRUG RESISTANT VARIANT R292K OF TERN N9 INFLUENZA VIRUS NEURAMINIDASE
 
Authors :  J. N. Varghese
Date :  07 Apr 98  (Deposition) - 11 Nov 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Neuraminidase, Influenza Protein, Drug Resistant Variant, Sialic Acid Analogues, Dana Anologues, Glycosylated Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. N. Varghese, P. W. Smith, S. L. Sollis, T. J. Blick, A. Sahasrabudhe, J. L. Mckimm-Breschkin, P. M. Colman
Drug Design Against A Shifting Target: A Structural Basis For Resistance To Inhibitors In A Variant Of Influenza Viru Neuraminidase.
Structure V. 6 735 1998
PubMed-ID: 9655825  |  Reference-DOI: 10.1016/S0969-2126(98)00075-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEURAMINIDASE
    Chains: A
    EC Number: 3.2.1.18
    Fragment: RESIDUES 82 - 468
    Mutation: YES
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
    Other Details: INTEGRAL MEMBRANE PROTEIN, MEMBRANE BOUND STALK CLEAVED BY PRONASE, RELEASING FULLY ACTIVE HEAD WITH RESIDUES 82 - 468
    Strain: A/TERN/AUSTRALIA/G70C/75
    Synonym: SIALIDASE
    Variant: NEURAMINIDASE R292K MUTATION (N2-TOKYO/3/67 NUMBERING)

 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, 13)

Asymmetric Unit (5, 13)
No.NameCountTypeFull Name
14AM1Ligand/Ion4-AMINO-2-DEOXY-2,3-DEHYDRO-N-NEURAMINIC ACID
2BMA1Ligand/IonBETA-D-MANNOSE
3CA2Ligand/IonCALCIUM ION
4MAN4Ligand/IonALPHA-D-MANNOSE
5NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 44)
No.NameCountTypeFull Name
14AM4Ligand/Ion4-AMINO-2-DEOXY-2,3-DEHYDRO-N-NEURAMINIC ACID
2BMA4Ligand/IonBETA-D-MANNOSE
3CA-1Ligand/IonCALCIUM ION
4MAN16Ligand/IonALPHA-D-MANNOSE
5NAG20Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:199 , ASN A:200 , LEU A:453 , GLY A:454 , GLN A:455 , NAG A:470B , HOH A:1078W , HOH A:1228K , HOH A:1292N , HOH A:1341RBINDING SITE FOR RESIDUE NAG A 469A
02AC2SOFTWAREGLN A:392 , GLY A:394 , NAG A:469A , BMA A:471C , HOH A:1026W , HOH A:1213K , HOH A:1228K , HOH A:1292NBINDING SITE FOR RESIDUE NAG A 470B
03AC3SOFTWARELEU A:377 , THR A:391 , GLN A:392 , GLY A:394 , NAG A:470B , MAN A:472D , MAN A:475G , HOH A:1074W , HOH A:1213KBINDING SITE FOR RESIDUE BMA A 471C
04AC4SOFTWAREARG A:364 , GLU A:375 , BMA A:471C , MAN A:473E , MAN A:474F , HOH A:1147F , HOH A:1283NBINDING SITE FOR RESIDUE MAN A 472D
05AC5SOFTWAREASP A:330 , ARG A:364 , LYS A:389 , PRO A:390 , MAN A:472D , MAN A:474F , HOH A:1260M , HOH A:1357RBINDING SITE FOR RESIDUE MAN A 473E
06AC6SOFTWAREARG A:327 , ASN A:329 , ASP A:330 , ARG A:364 , ILE A:366 , ILE A:368 , MAN A:472D , MAN A:473E , HOH A:1073W , HOH A:1144F , HOH A:1349RBINDING SITE FOR RESIDUE MAN A 474F
07AC7SOFTWAREBMA A:471C , HOH A:1209K , HOH A:1210K , HOH A:1329QBINDING SITE FOR RESIDUE MAN A 475G
08AC8SOFTWAREASP A:83 , PHE A:84 , ASN A:86 , ASN A:234 , NAG A:477B , HOH A:1179GBINDING SITE FOR RESIDUE NAG A 476A
09AC9SOFTWAREASP A:83 , NAG A:476ABINDING SITE FOR RESIDUE NAG A 477B
10BC1SOFTWAREASN A:146 , TRP A:437 , HOH A:1163FBINDING SITE FOR RESIDUE NAG A 478A
11BC2SOFTWAREASP A:293 , GLY A:297 , ASP A:324 , ASN A:347 , HOH A:1007W , HOH A:1088GBINDING SITE FOR RESIDUE CA A 999
12BC3SOFTWAREHOH A:1304P , HOH A:1392TBINDING SITE FOR RESIDUE CA A 989
13BC4SOFTWAREARG A:118 , GLU A:119 , ASP A:151 , ARG A:152 , ALA A:246 , GLU A:276 , LYS A:292 , ARG A:371 , TYR A:406 , HOH A:1086G , HOH A:1384T , HOH A:1385T , HOH A:1386T , HOH A:1396TBINDING SITE FOR RESIDUE 4AM A 800

(-) 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 2QWD)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QWD)

(-) 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 d2qwda_ A: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2qwdA00 A:82-468  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains Neur-2qwdA01 A:82-466                                                                                                                                                                                                                                                                                                                                                                             -- Pfam domains
         Sec.struct. author ..............eeeeeee..hhhhhhh.........eeeee..eeeeeeee.......hhh...........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee..............eee..eeeeeeeee.....eeeeeeeee..eeeeeee...........eeeee..eeeee..........eeeeee....eeeeee...........................................eeee.........eeeee.............eeeeee........eeee............eeeeeeeee.........eeeeeeeeeee..............hhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qwd A  82 RDFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRALISWPLSSPPTVYNSRVECIGWSSTSCHDGKTRMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESECVCHNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLAGTAKHIEECSCYGERAEITCTCKDNWQGSNRPVIRIDPVAMTHTSQYICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGVNTWLGRTISIASRSGYEMLKVPNALTDDKSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWDWPDGAKIEYFL 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        
                                                                                                                 169||                                                                                                                                                                333|                                                      392|               412|||                                                       
                                                                                                                  69A|                                                                                                                                                                 335                                                       394                12A||                                                       
                                                                                                                   170                                                                                                                                                                                                                                               12B|                                                       
                                                                                                                                                                                                                                                                                                                                                                      413
   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  (1, 1)

Asymmetric Unit
(-)
Clan: Sialidase (56)

(-) 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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  2qwd
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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 2qwe 2qwf 2qwg 2qwh 2qwi 2qwj 2qwk 3nn9 3w09 4dgr 4nn9 4weg 5nn9 6nn9 7nn9

(-) Related Entries Specified in the PDB File

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