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(-) Description

Title :  CRYSTAL STRUCTURE OF INFLUENZA A VIRUS NEURAMINIDASE N5 COMPLEXED WITH ZANAMIVIR
 
Authors :  M. Y. Wang, J. X. Qi, Y. Liu, C. J. Vavricka, Y. Wu, Q. Li, G. F. Gao
Date :  03 Jun 11  (Deposition) - 10 Aug 11  (Release) - 10 Aug 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, Hydrolase, Calcium Binding, Glycosylation, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Y. Wang, J. X. Qi, Y. Liu, C. J. Vavricka, Y. Wu, Q. Li, G. F. Gao
Influenza A Virus N5 Neuraminidase Has An Extended 150-Cavity
J. Virol. V. 85 8431 2011
PubMed-ID: 21653672  |  Reference-DOI: 10.1128/JVI.00638-11

(-) Compounds

Molecule 1 - NEURAMINIDASE
    Chains: A, B
    EC Number: 3.2.1.18
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Plasmid: PFASTBAC1
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 79-473
    Gene: NA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 385582
    Strain: A/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  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GOL4Ligand/IonGLYCEROL
3NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZMR2Ligand/IonZANAMIVIR
Biological Unit 1 (3, 24)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL8Ligand/IonGLYCEROL
3NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZMR4Ligand/IonZANAMIVIR
Biological Unit 2 (3, 24)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL8Ligand/IonGLYCEROL
3NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZMR4Ligand/IonZANAMIVIR

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:4 , ASP A:293 , GLY A:297 , ASP A:324 , TYR A:347 , HOH A:473BINDING SITE FOR RESIDUE CA A 601
02AC2SOFTWARELEU A:91 , ASN A:93 , HOH A:679 , NAG A:802 , HOH A:1048BINDING SITE FOR RESIDUE NAG A 801
03AC3SOFTWAREASN A:358 , NAG A:801 , HOH A:826 , HOH A:1091BINDING SITE FOR RESIDUE NAG A 802
04AC4SOFTWAREASN A:146 , HOH A:702 , HOH A:846BINDING SITE FOR RESIDUE NAG A 803
05AC5SOFTWAREHOH A:69 , 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 , GLU A:277 , ARG A:292 , ASN A:294 , TYR A:347 , ARG A:371 , TYR A:406 , HOH A:554 , HOH A:578 , HOH A:620 , HOH A:694BINDING SITE FOR RESIDUE ZMR A 901
06AC6SOFTWARELYS A:256 , ASN A:264 , HOH A:537 , HOH A:686 , HOH A:713 , HOH A:736 , HOH A:921 , ASN B:247 , TRP B:295BINDING SITE FOR RESIDUE GOL A 1
07AC7SOFTWARELYS A:286 , ILE A:304 , ASP A:306 , ASP A:311 , GLU A:313BINDING SITE FOR RESIDUE GOL A 472
08AC8SOFTWAREHOH B:3 , HOH B:43 , ASP B:293 , GLY B:297 , ASP B:324 , TYR B:347BINDING SITE FOR RESIDUE CA B 601
09AC9SOFTWARELEU B:91 , ASN B:93 , NAG B:802 , HOH B:999 , HOH B:1034 , HOH B:1046BINDING SITE FOR RESIDUE NAG B 801
10BC1SOFTWAREHOH A:492 , ASN B:358 , HOH B:619 , HOH B:656 , HOH B:702 , NAG B:801 , HOH B:913 , HOH B:949BINDING SITE FOR RESIDUE NAG B 802
11BC2SOFTWAREASN B:146 , HOH B:691BINDING SITE FOR RESIDUE NAG B 803
12BC3SOFTWAREARG 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:347 , ARG B:371 , TYR B:406 , HOH B:477 , HOH B:492 , HOH B:585 , HOH B:592 , HOH B:623 , HOH B:715BINDING SITE FOR RESIDUE ZMR B 901
13BC4SOFTWAREHOH B:7 , PHE B:115 , MET B:159 , SER B:164A , SER B:165 , ALA B:168 , GLN B:170 , ALA B:171BINDING SITE FOR RESIDUE GOL B 1
14BC5SOFTWAREASN B:87 , CYS B:124 , CYS B:183 , HIS B:184 , CYS B:230 , VAL B:231 , CYS B:232 , HOH B:489BINDING SITE FOR RESIDUE GOL 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: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 3SAN)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3SAN)

(-) 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 d3sana_ 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
                3san 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|                                   346A|                                    385|                       413A|||                                                         
                                                                                                                                                                                                                                                            308                                    346B                                     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 d3sanb_ 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
                3san 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|                                   346A|                                    385|                       413A|||                                                         
                                                                                                                                                                                                                                                            308                                    346B                                     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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  A1ILL9_I76A2 | A1ILL9
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        A1ILL9_I76A2 | A1ILL9: 3sal 3ti8

(-) Related Entries Specified in the PDB File

3nss STRUCTURE OF 09N1 NEURAMINIDASE
3sal