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(-) Description

Title :  CRYSTAL STRUCTURE OF INFLUENZA A VIRUS NEURAMINIDASE N5 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 :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  B  (4x)
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
    ChainsA, B
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System PlasmidPFASTBAC1
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentUNP RESIDUES 79-473
    GeneNA
    Organism ScientificINFLUENZA A VIRUS
    Organism Taxid385582
    StrainA/DUCK/ALBERTA/60/1976 H12N5

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (4x)A 
Biological Unit 2 (4x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2LNV2Ligand/Ion5-(ACETYLAMINO)-2,6-ANHYDRO-4-CARBAMIMIDAMIDO-3,4,5-TRIDEOXY-7-O-METHYL-D-GLYCERO-D-GALACTO-NON-2-ENONICACID
3NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2LNV4Ligand/Ion5-(ACETYLAMINO)-2,6-ANHYDRO-4-CARBAMIMIDAMIDO-3,4,5-TRIDEOXY-7-O-METHYL-D-GLYCERO-D-GALACTO-NON-2-ENONICACID
3NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 20)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2LNV4Ligand/Ion5-(ACETYLAMINO)-2,6-ANHYDRO-4-CARBAMIMIDAMIDO-3,4,5-TRIDEOXY-7-O-METHYL-D-GLYCERO-D-GALACTO-NON-2-ENONICACID
3NAG16Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:1 , HOH A:8 , ASP A:293 , GLY A:297 , ASP A:324 , TYR A:347BBINDING SITE FOR RESIDUE CA A 601
02AC2SOFTWARELEU A:91 , ASN A:93 , HOH A:737 , HOH A:907 , HOH A:1054BINDING SITE FOR RESIDUE NAG A 801
03AC3SOFTWAREASN A:146 , HOH A:554 , HOH A:731 , HOH A:732 , HOH A:1126BINDING SITE FOR RESIDUE NAG A 803
04AC4SOFTWAREHOH A:66 , ARG A:118 , GLU A:119 , ASP A:151 , ARG A:152 , ARG A:156 , TRP A:178 , ARG A:224 , GLU A:227 , ALA A:246 , GLU A:276 , ARG A:292 , ASN A:294 , TYR A:347B , ARG A:371 , TYR A:406 , HOH A:529 , HOH A:592 , HOH A:637 , HOH A:662 , HOH A:752BINDING SITE FOR RESIDUE LNV A 901
05AC5SOFTWAREHOH B:6 , HOH B:52 , ASP B:293 , GLY B:297 , ASP B:324 , TYR B:347BBINDING SITE FOR RESIDUE CA B 601
06AC6SOFTWARELEU B:91 , ASN B:93 , HOH B:716 , NAG B:802 , HOH B:820 , HOH B:1022BINDING SITE FOR RESIDUE NAG B 801
07AC7SOFTWAREASN B:358 , HOH B:560 , HOH B:716 , NAG B:801BINDING SITE FOR RESIDUE NAG B 802
08AC8SOFTWAREASN B:146 , HOH B:537 , HOH B:736 , NAG B:804 , HOH B:844 , HOH B:908 , HOH B:1003BINDING SITE FOR RESIDUE NAG B 803
09AC9SOFTWARENAG B:803 , HOH B:973BINDING SITE FOR RESIDUE NAG B 804
10BC1SOFTWAREHOH B:38 , ARG B:118 , GLU B:119 , ASP B:151 , ARG B:152 , ARG B:156 , TRP B:178 , ARG B:224 , GLU B:227 , ALA B:246 , GLU B:276 , GLU B:277 , ARG B:292 , ASN B:294 , TYR B:347B , ARG B:371 , TYR B:406 , HOH B:496 , HOH B:523 , HOH B:630BINDING SITE FOR RESIDUE LNV B 901

(-) 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:337
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:337
16B:421 -B:447

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Thr A:325 -Pro A:326
2Lys A:430 -Pro A:431
3Leu A:464 -Pro A:465
4Thr B:325 -Pro B:326
5Lys 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 3TI8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TI8)

(-) Exons   (0, 0)

(no "Exon" information available for 3TI8)

(-) 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:394
 aligned with A1ILL9_I76A2 | A1ILL9 from UniProtKB/TrEMBL  Length:473

    Alignment length:394
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468    
        A1ILL9_I76A2     79 PEFLNNTEPLCNVSGFAIVSKDNGIRIGSRGHVFVIREPFVACGPTECRTFFLTQGALLNDKHSNNTVKDRSPYRALMSVPLGSSPNAYQAKFESVAWSATACHDGKKWLAVGISGADDDAYAVIHYGGMPTDVVRSWRKQILRTQESSCVCMNGNCYWVMTDGPANSQASYKIFKSHEGMVTNEREVSFQGGHIEECSCYPNLGKVECVCRDNWNGMNRPILIFDEDLDYEVGYLCAGIPTDTPRVQDSSFTGSCTNAVGGSGTNNYGVKGFGFRQGNSVWAGRTVSISSRSGFEILLIEDGWIRTSKTIVKKVEVLNNKNWSGYSGAFTIPITMTSKQCLVPCFWLEMIRGKPEERTSIWTSSSSTVFCGVSSEVPGWSWDDGAILPFDIDK  472
               SCOP domains d3ti8a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhh.....eeeeeeeeee....eeeeeeeeeee..hhhhh..........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee..............eee..eeeeeeee.......eeeeeeee..eeeeeeee.......eeeeeeee..eeeeeee........eeeee.....eeeee............hhhhh.....................eeee..eeeeee.......eeeeeeee..........eeeeeeeeeeeee...eeeeeehhhhhh....eeeeeeeeeee.........eeeeeeeeeee................hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ti8 A   82 PEFLNNTEPLCNVSGFAIVSKDNGIRIGSRGHVFVIREPFVACGPTECRTFFLTQGALLNDKHSNNTVKDRSPYRALMSVPLGSSPNAYQAKFESVAWSATACHDGKKWLAVGISGADDDAYAVIHYGGMPTDVVRSWRKQILRTQESSCVCMNGNCYWVMTDGPANSQASYKIFKSHEGMVTNEREVSFQGGHIEECSCYPNLGKVECVCRDNWNGMNRPILIFDEDLDYEVGYLCAGIPTDTPRVQDSSFTGSCTNAVGGSGTNNYGVKGFGFRQGNSVWAGRTVSISSRSGFEILLIEDGWIRTSKTIVKKVEVLNNKNWSGYSGAFTIPITMTSKQCLVPCFWLEMIRGKPEERTSIWTSSSSTVFCGVSSEVPGWSWDDGAILPFDIDK  470
                                    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       341      |349       359       369       379     ||390       400       410   ||||416       426       436       446       456       466    
                                                                                                            164A                                                                                                                                           306|                                    347A|                                   385|                       413A|||                                                         
                                                                                                                                                                                                                                                            308                                     347B                                    387                        413B||                                                         
                                                                                                                                                                                                                                                                                                                                                                        413C|                                                         
                                                                                                                                                                                                                                                                                                                                                                         413D                                                         

Chain B from PDB  Type:PROTEIN  Length:394
 aligned with A1ILL9_I76A2 | A1ILL9 from UniProtKB/TrEMBL  Length:473

    Alignment length:394
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468    
        A1ILL9_I76A2     79 PEFLNNTEPLCNVSGFAIVSKDNGIRIGSRGHVFVIREPFVACGPTECRTFFLTQGALLNDKHSNNTVKDRSPYRALMSVPLGSSPNAYQAKFESVAWSATACHDGKKWLAVGISGADDDAYAVIHYGGMPTDVVRSWRKQILRTQESSCVCMNGNCYWVMTDGPANSQASYKIFKSHEGMVTNEREVSFQGGHIEECSCYPNLGKVECVCRDNWNGMNRPILIFDEDLDYEVGYLCAGIPTDTPRVQDSSFTGSCTNAVGGSGTNNYGVKGFGFRQGNSVWAGRTVSISSRSGFEILLIEDGWIRTSKTIVKKVEVLNNKNWSGYSGAFTIPITMTSKQCLVPCFWLEMIRGKPEERTSIWTSSSSTVFCGVSSEVPGWSWDDGAILPFDIDK  472
               SCOP domains d3ti8b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhh.....eeeeeeeeee....eeeeeeeeeee..hhhhh..........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee..............eee..eeeeeeee.......eeeeeeee..eeeeeeee.......eeeeeeee..eeeeeee........eeeee.....eeeee............hhhhh.....................eeee..eeeeee.......eeeeeeee..........eeeeeeeeeeeee...eeeeeehhhhhh....eeeeeeeeeee.........eeeeeeeeeee................hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ti8 B   82 PEFLNNTEPLCNVSGFAIVSKDNGIRIGSRGHVFVIREPFVACGPTECRTFFLTQGALLNDKHSNNTVKDRSPYRALMSVPLGSSPNAYQAKFESVAWSATACHDGKKWLAVGISGADDDAYAVIHYGGMPTDVVRSWRKQILRTQESSCVCMNGNCYWVMTDGPANSQASYKIFKSHEGMVTNEREVSFQGGHIEECSCYPNLGKVECVCRDNWNGMNRPILIFDEDLDYEVGYLCAGIPTDTPRVQDSSFTGSCTNAVGGSGTNNYGVKGFGFRQGNSVWAGRTVSISSRSGFEILLIEDGWIRTSKTIVKKVEVLNNKNWSGYSGAFTIPITMTSKQCLVPCFWLEMIRGKPEERTSIWTSSSSTVFCGVSSEVPGWSWDDGAILPFDIDK  470
                                    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       341      |349       359       369       379     ||390       400       410   ||||416       426       436       446       456       466    
                                                                                                            164A                                                                                                                                           306|                                    347A|                                   385|                       413A|||                                                         
                                                                                                                                                                                                                                                            308                                     347B                                    387                        413B||                                                         
                                                                                                                                                                                                                                                                                                                                                                        413C|                                                         
                                                                                                                                                                                                                                                                                                                                                                         413D                                                         

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TI8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TI8)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A1ILL9_I76A2 | A1ILL9)
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
        A1ILL9_I76A2 | A1ILL93sal 3san

(-) Related Entries Specified in the PDB File

3sal INFLUENZA A VIRUS NEURAMINIDASE N5 HAS AN EXTENDED 150- CAVITY
3san INFLUENZA A VIRUS NEURAMINIDASE N5 HAS AN EXTENDED 150- CAVITY
3ti3
3ti4
3ti5
3ti6
3tia
3tib
3tic