Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  THE STRUCTURE OF THE COMPLEX BETWEEN INFLUENZA VIRUS NEURAMINIDASE AND SIALIC ACID, THE VIRAL RECEPTOR
 
Authors :  J. N. Varghese, P. M. Colman
Date :  10 Aug 92  (Deposition) - 31 Jan 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Hydrolase(O-Glycosyl) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. N. Varghese, J. L. Mckimm-Breschkin, J. B. Caldwell, A. A. Kortt, P. M. Colman
The Structure Of The Complex Between Influenza Virus Neuraminidase And Sialic Acid, The Viral Receptor.
Proteins V. 14 327 1992
PubMed-ID: 1438172  |  Reference-DOI: 10.1002/PROT.340140302
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEURAMINIDASE N2
    Chains: A
    EC Number: 3.2.1.18
    Engineered: YES
    Organism Scientific: INFLUENZA A VIRUS (A/TOKYO/3/1967(H2N2))
    Organism Taxid: 380960
    Strain: A/TOKYO/3/1967(H2N2)

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 17)

Asymmetric Unit (7, 17)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CA1Ligand/IonCALCIUM ION
3FUL1Ligand/IonBETA-L-FUCOSE
4MAN4Ligand/IonALPHA-D-MANNOSE
5NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NGK1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-4-O-SULFO-ALPHA-D-GALACTOPYRANOSE
7SIA1Ligand/IonO-SIALIC ACID
Biological Unit 1 (6, 64)
No.NameCountTypeFull Name
1BMA8Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3FUL4Ligand/IonBETA-L-FUCOSE
4MAN16Ligand/IonALPHA-D-MANNOSE
5NAG28Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NGK4Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-4-O-SULFO-ALPHA-D-GALACTOPYRANOSE
7SIA4Ligand/IonO-SIALIC ACID

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:83 , ASN A:86 , SER A:88 , TYR A:284 , NAG A:484ABINDING SITE FOR RESIDUE NAG A 470A
02AC2SOFTWAREASN A:146 , TRP A:437 , NAG A:472B , FUL A:477IBINDING SITE FOR RESIDUE NAG A 471A
03AC3SOFTWARENAG A:471ABINDING SITE FOR RESIDUE NAG A 472B
04AC4SOFTWAREGLU A:433 , THR A:434 , ARG A:435 , ASN A:465 , HOH A:603BINDING SITE FOR RESIDUE NGK A 476F
05AC5SOFTWAREASN A:463 , NAG A:471ABINDING SITE FOR RESIDUE FUL A 477I
06AC6SOFTWAREASN A:200 , TYR A:453 , GLY A:454 , THR A:455 , NAG A:479B , HOH A:680BINDING SITE FOR RESIDUE NAG A 478A
07AC7SOFTWAREASN A:393 , ARG A:394 , NAG A:478A , BMA A:480C , MAN A:481D , HOH A:672BINDING SITE FOR RESIDUE NAG A 479B
08AC8SOFTWAREGLN A:391 , ILE A:392 , ASN A:393 , ARG A:394 , NAG A:479B , MAN A:481D , MAN A:482E , MAN A:483FBINDING SITE FOR RESIDUE BMA A 480C
09AC9SOFTWAREGLN A:391 , NAG A:479B , BMA A:480C , MAN A:482E , HOH A:665BINDING SITE FOR RESIDUE MAN A 481D
10BC1SOFTWAREBMA A:480C , MAN A:481DBINDING SITE FOR RESIDUE MAN A 482E
11BC2SOFTWAREBMA A:480CBINDING SITE FOR RESIDUE MAN A 483F
12BC3SOFTWAREASN A:234 , TYR A:284 , NAG A:470ABINDING SITE FOR RESIDUE NAG A 484A
13BC4SOFTWAREARG A:118 , GLU A:119 , ASP A:151 , ARG A:152 , ALA A:246 , GLU A:276 , GLU A:277 , ARG A:292 , ARG A:371 , TYR A:406 , HOH A:699XBINDING SITE FOR RESIDUE SIA A 600
14BC5SOFTWAREASP A:293 , GLY A:297 , ASP A:324 , GLY A:345 , GLN A:347BINDING SITE FOR RESIDUE CA A 601

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:92 -A:417
2A:124 -A:129
3A:175 -A:193
4A:183 -A:230
5A:232 -A:237
6A:278 -A:291
7A:280 -A:289
8A:318 -A:337
9A:421 -A:447

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Tyr A:284 -Pro A:285
2Thr A:325 -Pro A:326
3Arg A:430 -Lys A:431

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BAT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BAT)

(-) Exons   (0, 0)

(no "Exon" information available for 2BAT)

(-) 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:388
 aligned with NRAM_I67A0 | P06820 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:388
                                    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        
           NRAM_I67A0    82 VEYRNWSKPQCQITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPVKCYQFALGQGTTLDNKHSNDTVHDRIPHRTLLMNELGVPFHLGTRQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYDGRLVDSIGSWSQNILRTQESECVCINGTCTVVMTDGSASGRADTRILFIEEGKIVHISPLAGSAQHVEECSCYPRYPGVRCICRDNWKGSNRPVVDINMEDYSIDSSYVCSGLVGDTPRNDDRSSNSNCRNPNNERGTQGVKGWAFDNGNDLWMGRTISKDLRSGYETFKVIGGWSTPNSKSQINRQVIVDSDNRSGYSGIFSVEGKSCINRCFYVELIRGRKQETRVWWTSNSIVVFCGTSGTYGTGSWPDGANINFMPI 469
               SCOP domains d2bata_ A: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2batA00 A:82-469  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhhhhh..eeeeeeeeee....eeeeeeeeeee..hhhhh..........eeeeee.........eeeee...eeeee....eeeeeee.hhhh.eeeeee..eeeeeee.......ee.....eee..eeeeeeeee.....eeeeeeeee..eeeeeee........eeeeeeee..eeeeeee........eeeeee.....eeeee............hhhhh...................eeee..eeeeeee......eeeeeeeee.........eeeeeeeeeeeeee...eeeeeee....eeeeeeeeeeee.........eeeeeeeeeee.............hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bat A  82 VEYRNWSKPQCQITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPVKCYQFALGQGTTLDNKHSNDTVHDRIPHRTLLMNELGVPFHLGTRQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYDGRLVDSIGSWSQNILRTQESECVCINGTCTVVMTDGSASGRADTRILFIEEGKIVHISPLAGSAQHVEECSCYPRYPGVRCICRDNWKGSNRPVVDINMEDYSIDSSYVCSGLVGDTPRNDDRSSNSNCRNPNNERGTQGVKGWAFDNGNDLWMGRTISKDLRSGYETFKVIGGWSTPNSKSQINRQVIVDSDNRSGYSGIFSVEGKSCINRCFYVELIRGRKQETRVWWTSNSIVVFCGTSGTYGTGSWPDGANINFMPI 469
                                    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
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BAT)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (NRAM_I67A0 | P06820)
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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FUL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NGK  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SIA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:430 - Lys A:431   [ RasMol ]  
    Thr A:325 - Pro A:326   [ RasMol ]  
    Tyr A:284 - Pro A:285   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2bat
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NRAM_I67A0 | P06820
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.18
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  NRAM_I67A0 | P06820
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NRAM_I67A0 | P06820: 1ing 1inh 1inw 1inx 1ivc 1ivd 1ive 1ivf 1ivg 1nn2

(-) Related Entries Specified in the PDB File

1nn2 NATIVE