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(-) Description

Title :  CRYSTAL STRUCTURE OF 2009 PANDEMIC H1N1 NEURAMINIDASE COMPLEXED WITH LANINAMIVIR
 
Authors :  C. J. Vavricka, Q. Li, Y. Wu, J. Qi, M. Wang, Y. Liu, F. Gao, J. Liu, E. Feng, J. Wang, H. Liu, H. Jiang, G. F. Gao
Date :  20 Aug 11  (Deposition) - 16 Nov 11  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  6-Bladed Beta-Propeller, Calcium Binding, Glycosylation, Antiviral, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Vavricka, Q. Li, Y. Wu, J. Qi, M. Wang, Y. Liu, F. Gao, J. Liu, E. Feng J. He, J. Wang, H. Liu, H. Jiang, G. F. Gao
Structural And Functional Analysis Of Laninamivir And Its Octanoate Prodrug Reveals Group Specific Mechanisms For Influenza Na Inhibition
Plos Pathog. V. 7 02249 2011
PubMed-ID: 22028647  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1002249

(-) Compounds

Molecule 1 - NEURAMINIDASE
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Plasmid: PACGP67-B
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 82-469
    Gene: NA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 641501
    Strain: A/CALIFORNIA/04/2009(H1N1)

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 17)

Asymmetric Unit (5, 17)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CA5Ligand/IonCALCIUM ION
3GOL3Ligand/IonGLYCEROL
4LNV2Ligand/Ion5-(ACETYLAMINO)-2,6-ANHYDRO-4-CARBAMIMIDAMIDO-3,4,5-TRIDEOXY-7-O-METHYL-D-GLYCERO-D-GALACTO-NON-2-ENONICACID
5NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 24)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3GOL6Ligand/IonGLYCEROL
4LNV4Ligand/Ion5-(ACETYLAMINO)-2,6-ANHYDRO-4-CARBAMIMIDAMIDO-3,4,5-TRIDEOXY-7-O-METHYL-D-GLYCERO-D-GALACTO-NON-2-ENONICACID
5NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:146 , NAG A:502 , HOH A:524 , HOH A:966 , HOH A:983 , HOH A:1256BINDING SITE FOR RESIDUE NAG A 501
02AC2SOFTWARENAG A:501 , HOH A:857 , ASN B:329 , HOH B:674BINDING SITE FOR RESIDUE NAG A 502
03AC3SOFTWAREASN A:88 , HOH A:513 , HOH A:552 , HOH A:845 , HOH A:1181BINDING SITE FOR RESIDUE NAG A 505
04AC4SOFTWAREHOH A:4 , ASP A:293 , GLY A:297 , ASP A:324 , GLY A:345 , ASN A:347BINDING SITE FOR RESIDUE CA A 601
05AC5SOFTWAREHOH A:42 , ASP A:379 , ASN A:381 , ASP A:387 , ASN A:389 , HOH A:689BINDING SITE FOR RESIDUE CA A 602
06AC6SOFTWAREHOH A:1302 , HOH B:716 , HOH B:1035BINDING SITE FOR RESIDUE CA A 603
07AC7SOFTWAREARG A:118 , GLU A:119 , ASP A:151 , ARG A:152 , ARG A:156 , TRP A:178 , ARG A:224 , GLU A:227 , SER A:246 , GLU A:276 , GLU A:277 , ARG A:292 , ASN A:294 , ARG A:371 , TYR A:406 , HOH A:512 , HOH A:556 , HOH A:657 , HOH A:823 , HOH A:873BINDING SITE FOR RESIDUE LNV A 801
08AC8SOFTWARETRP A:403 , ILE A:427 , GLY A:429 , ARG A:430 , PRO A:431 , LYS A:432 , GLU A:433 , HOH A:545 , HOH A:606BINDING SITE FOR RESIDUE GOL A 1
09AC9SOFTWARELEU A:127 , GLU A:128 , CYS A:129 , HOH A:498 , HOH A:661 , ASN B:208 , ILE B:210BINDING SITE FOR RESIDUE GOL A 471
10BC1SOFTWARESER A:95 , GLN A:395 , THR A:453 , HOH A:1221BINDING SITE FOR RESIDUE ACT A 472
11BC2SOFTWAREASN B:88 , HOH B:523 , HOH B:575 , HOH B:756 , HOH B:783 , HOH B:789 , HOH B:823 , HOH B:1271BINDING SITE FOR RESIDUE NAG B 505
12BC3SOFTWAREHOH B:28 , ASP B:293 , GLY B:297 , ASP B:324 , GLY B:345 , ASN B:347BINDING SITE FOR RESIDUE CA B 601
13BC4SOFTWAREHOH B:38 , ASP B:379 , ASN B:381 , ASP B:387 , ASN B:389 , HOH B:649BINDING SITE FOR RESIDUE CA B 602
14BC5SOFTWAREHOH B:67 , ARG B:118 , GLU B:119 , ASP B:151 , ARG B:152 , ARG B:156 , TRP B:178 , ARG B:224 , GLU B:227 , SER B:246 , GLU B:276 , GLU B:277 , ARG B:292 , ASN B:294 , ARG B:371 , TYR B:406 , HOH B:490 , HOH B:501 , HOH B:631 , HOH B:890BINDING SITE FOR RESIDUE LNV B 801
15BC6SOFTWARETRP B:403 , ILE B:427 , GLY B:429 , ARG B:430 , PRO B:431 , LYS B:432 , GLU B:433 , HOH B:583BINDING SITE FOR RESIDUE ACT B 1
16BC7SOFTWAREASN A:208 , GLY A:209 , ILE A:210 , TYR B:100 , LEU B:127 , GLU B:128 , CYS B:129 , ILE B:163 , LEU B:412D , HOH B:808BINDING SITE FOR RESIDUE GOL B 471
17BC8SOFTWARESER B:95 , GLN B:395 , THR B:453 , HOH B:1281BINDING SITE FOR RESIDUE ACT B 472

(-) SS Bonds  (16, 16)

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:336
8A:421 -A:447
9B:92 -B:417
10B:124 -B:129
11B:183 -B:230
12B:232 -B:237
13B:278 -B:291
14B:280 -B:289
15B:318 -B:336
16B:421 -B:447

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Asn A:325 -Pro A:326
2Arg A:430 -Pro A:431
3Leu A:464 -Pro A:465
4Asn B:325 -Pro B:326
5Arg B:430 -Pro B:431
6Leu B:464 -Pro B:465

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TI3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TI3)

(-) Exons   (0, 0)

(no "Exon" information available for 3TI3)

(-) 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:387
 aligned with C3W5S3_I09A0 | C3W5S3 from UniProtKB/TrEMBL  Length:469

    Alignment length:387
                                    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       
        C3W5S3_I09A0     82 SVKLAGNSSLCPVSGWAIYSKDNSVRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQDIVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTID  468
               SCOP domains d3ti3a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhhh....eeeeeeeeee....eeeeeeeeeee..hhhhh..........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee..............eee..eeeeeeee.......eeeeeeee..eeeeeee........eeeeeeee..eeeeeee........eeeee.....eeeee.................................eeee..eeeeee.......eeeeeeee............eeeeeeeeeee...eeeeeehhhhhh....eeeeeeeeeee........eeeeeeeeeee.................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ti3 A   82 SVKLAGNSSLCPVSGWAIYSKDNSVRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQDIVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTID  469
                                    91       101       111       121       131       141       151       161       170       180       190       200       210       220       230       240       250       260       270       280       290       300     ||311       321       331 ||||  344       354       364       374       384       395       405      412C|      421       431 ||    442       452       462       
                                                                                                                 169A                                                                                                                                      306|                      333|||                                                  392|               412A|||                  433|                                  
                                                                                                                                                                                                                                                            308                       335||                                                   394                412B||                   435                                  
                                                                                                                                                                                                                                                                                       336|                                                                       412C|                                                        
                                                                                                                                                                                                                                                                                        339                                                                        412D                                                        


Chain B from PDB  Type:PROTEIN  Length:387
 aligned with C3W5S3_I09A0 | C3W5S3 from UniProtKB/TrEMBL  Length:469

    Alignment length:387
                                    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       
        C3W5S3_I09A0     82 SVKLAGNSSLCPVSGWAIYSKDNSVRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQDIVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTID  468
               SCOP domains d3ti3b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhhh....eeeeeeeeee....eeeeeeeeeee..hhhhh..........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee..............eee..eeeeeeee.......eeeeeeee..eeeeeee........eeeeeeee..eeeeeee........eeeee.....eeeee.................................eeee..eeeeee.......eeeeeeee............eeeeeeeeeee...eeeeeehhhhhh....eeeeeeeeeee........eeeeeeeeeee.................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ti3 B   82 SVKLAGNSSLCPVSGWAIYSKDNSVRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQDIVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTID  469
                                    91       101       111       121       131       141       151       161       170       180       190       200       210       220       230       240       250       260       270       280       290       300     ||311       321       331 ||||  344       354       364       374       384       395       405      412C|      421       431 ||    442       452       462       
                                                                                                                 169A                                                                                                                                      306|                      333|||                                                  392|               412A|||                  433|                                  
                                                                                                                                                                                                                                                            308                       335||                                                   394                412B||                   435                                  
                                                                                                                                                                                                                                                                                       336|                                                                       412C|                                                        
                                                                                                                                                                                                                                                                                        339                                                                        412D
   Legend:   → Mismatch (orange background)
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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, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TI3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TI3)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (C3W5S3_I09A0 | C3W5S3)
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/TrEMBL
        C3W5S3_I09A0 | C3W5S3: 3nss 3ti4 3ti5 3ti6

(-) Related Entries Specified in the PDB File

3nss THE 2009 PANDEMIC H1N1 NEURAMINIDASE N1 LACKS THE 150- CAVITY IN ITS ACTIVE SITES
3ti4
3ti5
3ti6
3ti8
3tia
3tib
3tic