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(-) Description

Title :  INFLUENZA B VIRUS NEURAMINIDASE CAN SYNTHESIZE ITS OWN INHIBITOR
 
Authors :  W. P. Burmeister, R. W. H. Ruigrok, S. Cusack
Date :  24 May 93  (Deposition) - 31 Oct 93  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  O-Glycosyl, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. P. Burmeister, B. Henrissat, C. Bosso, S. Cusack, R. W. Ruigrok
Influenza B Virus Neuraminidase Can Synthesize Its Own Inhibitor.
Structure V. 1 19 1993
PubMed-ID: 8069621  |  Reference-DOI: 10.1016/0969-2126(93)90005-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEURAMINIDASE
    Chains: A, B
    EC Number: 3.2.1.18
    Engineered: YES
    Organism Scientific: INFLUENZA B VIRUS (STRAIN B/BEIJING/1/87)
    Organism Taxid: 11525
    Strain: B/BEIJING/1/87

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2DAN2Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DAN4Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:81 , PRO A:82 , ASN A:283 , HOH A:553 , HOH A:702BINDING SITE FOR RESIDUE NAG A 466
02AC2SOFTWARETYR B:81 , PRO B:82 , ASN B:283 , HOH B:512BINDING SITE FOR RESIDUE NAG B 466
03AC3SOFTWAREASP A:292 , THR A:296 , ASP A:323 , GLY A:343 , GLY A:345 , HOH A:648BINDING SITE FOR RESIDUE CA A 468
04AC4SOFTWAREASP B:292 , THR B:296 , ASP B:323 , GLY B:343 , GLY B:345 , HOH B:572BINDING SITE FOR RESIDUE CA B 469
05AC5SOFTWAREGLU A:167 , GLU B:167 , HOH B:539BINDING SITE FOR RESIDUE CA A 470
06AC6SOFTWAREARG A:115 , GLU A:116 , ASP A:148 , ARG A:149 , ARG A:222 , ALA A:244 , GLU A:274 , GLU A:275 , ARG A:291 , ARG A:373 , TYR A:408 , HOH A:682 , HOH A:683 , HOH A:685 , HOH A:688 , HOH A:689BINDING SITE FOR RESIDUE DAN A 467
07AC7SOFTWAREARG B:115 , GLU B:116 , ASP B:148 , ARG B:149 , ARG B:222 , GLU B:274 , ARG B:291 , ARG B:373 , TYR B:408 , HOH B:680 , HOH B:683 , HOH B:684 , HOH B:685 , HOH B:686 , HOH B:688BINDING SITE FOR RESIDUE DAN B 467
08CHAAUTHORASP A:323 , GLY A:343 , GLY A:345 , THR A:296 , ASP A:292HIGH-AFFINITY CALCIUM-BINDING SITES
09CHBAUTHORASP B:323 , GLY B:343 , GLY B:345 , THR B:296 , ASP B:292HIGH-AFFINITY CALCIUM-BINDING SITES
10CLAAUTHORGLU A:167LOW-AFFINITY CALCIUM-BINDING SITES
11CLBAUTHORGLU B:167LOW-AFFINITY CALCIUM-BINDING SITES
12NEAAUTHORASP A:323 , ARG A:115 , ARG A:291 , ARG A:149 , ILE A:220 , ARG A:222 , TRP A:176 , GLU A:274 , ASP A:148 , TYR A:408ACTIVE SITE
13NEBAUTHORASP B:323 , ARG B:115 , ARG B:291 , ARG B:149 , ILE B:220 , ARG B:222 , TRP B:176 , GLU B:274 , ASP B:148 , TYR B:408ACTIVE SITE

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:86 -A:419
2A:121 -A:126
3A:181 -A:228
4A:230 -A:235
5A:276 -A:290
6A:278 -A:288
7A:317 -A:336
8A:423 -A:446
9B:86 -B:419
10B:121 -B:126
11B:181 -B:228
12B:230 -B:235
13B:276 -B:290
14B:278 -B:288
15B:317 -B:336
16B:423 -B:446

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gln A:137 -Pro A:138
2Thr A:324 -Pro A:325
3Gln B:137 -Pro B:138
4Thr B:324 -Pro B:325

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NSD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NSD)

(-) Exons   (0, 0)

(no "Exon" information available for 1NSD)

(-) 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:390
 aligned with NRAM_INBBE | P27907 from UniProtKB/Swiss-Prot  Length:465

    Alignment length:390
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465
           NRAM_INBBE    76 EPEWTYPRLSCQGSTFQKALLISPHRFGEARGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALIKIKYGEAYTDTYHSYANNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIECACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGRGGIKGGFVHQRMASKIGRWYSRTMSKTERMGMELYVRYDGDPWTDSDALAHSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHDGGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL 465
               SCOP domains d1nsda_ A: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1nsdA00 A:76-465  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............eeeeeeehhhhhh.........eeeeeeeee....eeeeeee.....................eeeeee..........eeeee..eeeeee....eeeeeee.hhhh.eeeeee..eeeeeee.......ee.....eee..eeeeeeeee.....eeeeeeeee..eeeeee.........eeeeeee....eeeeeee........eeeeee....eeeeee...................................eeeee....eeeeeee.........eeeeeee...........eeeeeee........eeeeeee....eeeeeeeeeee........eeeeeeeee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nsd A  76 EPEWTYPRLSCQGSTFQKALLISPHRFGEARGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALIKIKYGEAYTDTYHSYANNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIECACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGRGGIKGGFVHQRMASKIGRWYSRTMSKTERMGMELYVRYDGDPWTDSDALAHSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHDGGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL 465
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465


Chain B from PDB  Type:PROTEIN  Length:390
 aligned with NRAM_INBBE | P27907 from UniProtKB/Swiss-Prot  Length:465

    Alignment length:390
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465
           NRAM_INBBE    76 EPEWTYPRLSCQGSTFQKALLISPHRFGEARGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALIKIKYGEAYTDTYHSYANNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIECACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGRGGIKGGFVHQRMASKIGRWYSRTMSKTERMGMELYVRYDGDPWTDSDALAHSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHDGGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL 465
               SCOP domains d1nsdb_ B: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1nsdB00 B:76-465  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............eeeeeeehhhhhh.........eeeeeeeee....eeeeeee.....................eeeeee..........eeeee..eeeeee....eeeeeee.hhhh.eeeeee..eeeeeee.......ee.....eee..eeeeeeeee.....eeeeeeeee..eeeeee.........eeeeeee....eeeeeee........eeeeee....eeeeee...................................eeeee....eeeeeee.........eeeeeee...........eeeeeee........eeeeeee....eeeeeeeeeee........eeeeeeeee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nsd B  76 EPEWTYPRLSCQGSTFQKALLISPHRFGEARGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALIKIKYGEAYTDTYHSYANNILRTQESACNCIGGDCYLMITDGSASGISKCRFLKIREGRIIKEIFPTGRVEHTEECTCGFASNKTIECACRDNSYTAKRPFVKLNVETDTAEIRLMCTETYLDTPRPDDGSITGPCESNGDKGRGGIKGGFVHQRMASKIGRWYSRTMSKTERMGMELYVRYDGDPWTDSDALAHSGVMVSMKEPGWYSFGFEIKDKKCDVPCIGIEMVHDGGKKTWHSAATAIYCLMGSGQLLWDTVTGVDMAL 465
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465
   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  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1NSD)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NRAM_INBBE | P27907)
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)

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        NRAM_INBBE | P27907: 1a4g 1a4q 1nsb 1nsc

(-) Related Entries Specified in the PDB File

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