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(-) Description

Title :  CRYSTAL STRUCTURE OF B/PERTH NEURAMINIDASE
 
Authors :  A. J. Oakley, J. L. Mckimm-Breschkin
Date :  02 Oct 09  (Deposition) - 01 Sep 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  B  (4x)
Keywords :  Influenza, Neuraminidase, Mutation, Resistance, Hydrolase, Cell Membrane, Glycosidase, Membrane, Transmembrane, Virion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Oakley, S. Barrett, T. S. Peat, J. Newman, V. A. Streltsov, L. Waddington, T. Saito, M. Tashiro, J. L. Mckimm-Breschkin
Structural And Functional Basis Of Resistance To Neuraminidase Inhibitors Of Influenza B Viruses.
J. Med. Chem. 2010
PubMed-ID: 20695427  |  Reference-DOI: 10.1021/JM100621S

(-) Compounds

Molecule 1 - NEURAMINIDASE
    Chains: A, B
    EC Number: 3.2.1.18
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF21
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector: PFASTBAC
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 70-466
    Organism Common: VIRUSES
    Organism Scientific: INFLUENZA B VIRUS
    Organism Taxid: 343983
    Strain: B/PERTH/211/2001

 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  (7, 22)

Asymmetric Unit (7, 22)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CA2Ligand/IonCALCIUM ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
4GOL4Ligand/IonGLYCEROL
5MAN6Ligand/IonALPHA-D-MANNOSE
6NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SO42Ligand/IonSULFATE ION
Biological Unit 1 (6, 36)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3EDO4Ligand/Ion1,2-ETHANEDIOL
4GOL4Ligand/IonGLYCEROL
5MAN12Ligand/IonALPHA-D-MANNOSE
6NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SO44Ligand/IonSULFATE ION
Biological Unit 2 (6, 44)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3EDO4Ligand/Ion1,2-ETHANEDIOL
4GOL12Ligand/IonGLYCEROL
5MAN12Ligand/IonALPHA-D-MANNOSE
6NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SO44Ligand/IonSULFATE ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARENAG A:2 , PRO A:83 , ARG A:84 , ASN A:284 , ARG A:356 , HOH A:489BINDING SITE FOR RESIDUE NAG A 1
02AC2SOFTWARENAG A:1 , BMA A:3 , MAN A:4 , MAN A:6 , LEU A:85 , HOH A:489 , TYR B:82BINDING SITE FOR RESIDUE NAG A 2
03AC3SOFTWARENAG A:2 , MAN A:4BINDING SITE FOR RESIDUE BMA A 3
04AC4SOFTWARENAG A:2 , BMA A:3 , MAN A:5 , MAN A:6 , TRP B:80 , TYR B:82 , GLY B:233 , ARG B:257BINDING SITE FOR RESIDUE MAN A 4
05AC5SOFTWAREMAN A:4 , ASN B:235 , TYR B:237 , LYS B:255 , VAL B:307BINDING SITE FOR RESIDUE MAN A 5
06AC6SOFTWARENAG A:2 , MAN A:4 , GLU B:79BINDING SITE FOR RESIDUE MAN A 6
07AC7SOFTWAREARG A:116 , ARG A:292 , ARG A:374 , TYR A:409 , HOH A:565BINDING SITE FOR RESIDUE SO4 A 467
08AC8SOFTWAREHOH A:62 , CYS A:122 , GLY A:123 , PRO A:124 , LYS A:125 , CYS A:127 , GLU A:208 , LYS A:416BINDING SITE FOR RESIDUE EDO A 468
09AC9SOFTWARESER A:370 , THR A:372 , LYS A:373 , HOH A:547 , ASP B:463 , MET B:464 , ALA B:465BINDING SITE FOR RESIDUE GOL A 469
10BC1SOFTWAREASP A:293 , THR A:297 , ASP A:324 , GLY A:344 , GLY A:346 , HOH A:529BINDING SITE FOR RESIDUE CA A 470
11BC2SOFTWARENAG B:2 , PRO B:83 , LEU B:85 , ASN B:284 , ARG B:356 , HOH B:539BINDING SITE FOR RESIDUE NAG B 1
12BC3SOFTWARETYR A:82 , NAG B:1 , BMA B:3 , MAN B:4 , LEU B:85 , HOH B:539BINDING SITE FOR RESIDUE NAG B 2
13BC4SOFTWARENAG B:2 , MAN B:4 , MAN B:5BINDING SITE FOR RESIDUE BMA B 3
14BC5SOFTWARETRP A:80 , TYR A:82 , GLY A:233 , ASN A:235 , ARG A:257 , NAG B:2 , BMA B:3 , MAN B:5 , MAN B:6BINDING SITE FOR RESIDUE MAN B 4
15BC6SOFTWAREILE A:232 , ASN A:235 , LYS A:255 , VAL A:307 , HOH A:520 , BMA B:3 , MAN B:4BINDING SITE FOR RESIDUE MAN B 5
16BC7SOFTWAREGLU A:79 , MAN B:4BINDING SITE FOR RESIDUE MAN B 6
17BC8SOFTWAREARG B:116 , ARG B:292 , ARG B:374 , TYR B:409BINDING SITE FOR RESIDUE SO4 B 467
18BC9SOFTWAREVAL B:399 , LEU B:454 , LEU B:455BINDING SITE FOR RESIDUE EDO B 468
19CC1SOFTWARETYR B:214 , HIS B:215 , SER B:216 , TYR B:217BINDING SITE FOR RESIDUE GOL B 469
20CC2SOFTWARECYS B:122 , GLY B:123 , PRO B:124 , CYS B:127 , GLU B:208 , ILE B:415 , LYS B:416 , HOH B:563BINDING SITE FOR RESIDUE GOL B 470
21CC3SOFTWAREASP A:463 , MET A:464 , ALA A:465 , SER B:370 , LYS B:371 , THR B:372 , LYS B:373 , HOH B:535BINDING SITE FOR RESIDUE GOL B 471
22CC4SOFTWAREASP B:293 , THR B:297 , ASP B:324 , GLY B:344 , GLY B:346BINDING SITE FOR RESIDUE CA B 472

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:87 -A:420
2A:122 -A:127
3A:182 -A:229
4A:231 -A:236
5A:277 -A:291
6A:279 -A:289
7A:318 -A:337
8A:424 -A:447
9B:87 -B:420
10B:122 -B:127
11B:182 -B:229
12B:231 -B:236
13B:277 -B:291
14B:279 -B:289
15B:318 -B:337
16B:424 -B:447

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gln A:138 -Pro A:139
2Thr A:325 -Pro A:326
3Gln B:138 -Pro B:139
4Thr B:325 -Pro B:326

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K36)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K36)

(-) Exons   (0, 0)

(no "Exon" information available for 3K36)

(-) 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:389
 aligned with Q3S340_9INFB | Q3S340 from UniProtKB/TrEMBL  Length:466

    Alignment length:389
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457         
         Q3S340_9INFB    78 PEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTRGDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDNNALLKIKYGEAYTDTYHSYANNILRTQESACNCIGGNCYLMITDGSASGISECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIECACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGSGGIKGGFVHQRMASKIGRWYSRTMSKTKRMGMGLYVKYDGDPWTDSDALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHDGGKETWHSAATAIYCLMGSGQLLWDTVTGVDMAL 466
               SCOP domains d3k36a_ A: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeehhhhhh........eeeeeeeeee....eeeeeeeeeee.................eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee.......ee.....eee..eeeeeee..........eeeeee..eeeeee..ee.....eeeeeee....eeeeeee........eeeeee....eeeeee...................................eeeeee..eeeeeeee.......eeeeeeeee...........eeeeeeeeeeee...eeeeeee....eeeeeeeeeee........eeeeeeeee.................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k36 A  78 PEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTRGDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDNNALLKIKYGEAYTDTYHSYANNILRTQESACNCIGGNCYLMITDGSASGISECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIECACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGSGGIKGGFVHQRMASKIGRWYSRTMSKTKRMGMGLYVKYDGDPWTDSDALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHDGGKETWHSAATAIYCLMGSGQLLWDTVTGVDMAL 466
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457         


Chain B from PDB  Type:PROTEIN  Length:389
 aligned with Q3S340_9INFB | Q3S340 from UniProtKB/TrEMBL  Length:466

    Alignment length:389
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457         
         Q3S340_9INFB    78 PEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTRGDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDNNALLKIKYGEAYTDTYHSYANNILRTQESACNCIGGNCYLMITDGSASGISECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIECACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGSGGIKGGFVHQRMASKIGRWYSRTMSKTKRMGMGLYVKYDGDPWTDSDALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHDGGKETWHSAATAIYCLMGSGQLLWDTVTGVDMAL 466
               SCOP domains d3k36b_ B: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Neur-3k36B01 B:78-466                                                                                                                                                                                                                                                                                                                                                                                 Pfam domains (1)
           Pfam domains (2) Neur-3k36B02 B:78-466                                                                                                                                                                                                                                                                                                                                                                                 Pfam domains (2)
         Sec.struct. author ..............eeeeeeehhhhhh........eeeeeeeeee....eeeeeeeeeee.................eeeeee..........eeeee..eeeeee....eeeeeee.hhhh.eeeeee..eeeeeee.......ee.....eee..eeeeeee..........eeeeee..eeeeee..ee.....eeeeeee....eeeeeee........eeeeee....eeeeee...................................eeeee....eeeeeee.......eeeeeeeee...........eeeeeeeeeeee...eeeeeee....eeeeeeeeeee........eeeeeeeee.................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k36 B  78 PEWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTRGDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDNNALLKIKYGEAYTDTYHSYANNILRTQESACNCIGGNCYLMITDGSASGISECRFLKIREGRIIKEIFPTGRVKHTEECTCGFASNKTIECACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGSGGIKGGFVHQRMASKIGRWYSRTMSKTKRMGMGLYVKYDGDPWTDSDALALSGVMVSMEEPGWYSFGFEIKDKKCDVPCIGIEMVHDGGKETWHSAATAIYCLMGSGQLLWDTVTGVDMAL 466
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457
   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 3K36)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Sialidase (56)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q3S340_9INFB | Q3S340)
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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  3k36
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  Q3S340_9INFB | Q3S340
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  3.2.1.18
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 Related Entries

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

UniProtKB/TrEMBL
        Q3S340_9INFB | Q3S340: 3k37 3k38 3k39 3k3a

(-) Related Entries Specified in the PDB File

3k37 3k38 3k39 3k3a