Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
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 :  N2 NEURAMINIDASE OF A/TANZANIA/205/2010 H3N2 IN COMPLEX WITH OSELTAMIVIR CARBOXYLATE
 
Authors :  X. Zhu, I. A. Wilson
Date :  06 Sep 12  (Deposition) - 17 Oct 12  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Beta-Propella, Influenza Virus, Neuraminidase, Hemagglutinin, Hemadsorption, Viral Infection, Sialic Acid Receptor, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zhu, R. Mcbride, C. M. Nycholat, W. Yu, J. C. Paulson, I. A. Wilson
Influenza Virus Neuraminidases With Reduced Enzymatic Activity That Avidly Bind Sialic Acid Receptors.
J. Virol. V. 86 13371 2012
PubMed-ID: 23015718  |  Reference-DOI: 10.1128/JVI.01426-12

(-) Compounds

Molecule 1 - NEURAMINIDASE
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Plasmid: PFASTBACHT-A
    Expression System Taxid: 7111
    Expression System Vector Type: PLASMID
    Fragment: ECTODOMAIN
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 119210
    Strain: A/TANZANIA/205/2010(H3N2)

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric Unit (5, 12)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA2Ligand/IonCALCIUM ION
3G391Ligand/Ion(3R,4R,5S)-4-(ACETYLAMINO)-5-AMINO-3-(PENTAN-3-YLOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID
4MAN2Ligand/IonALPHA-D-MANNOSE
5NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 40)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3G394Ligand/Ion(3R,4R,5S)-4-(ACETYLAMINO)-5-AMINO-3-(PENTAN-3-YLOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID
4MAN8Ligand/IonALPHA-D-MANNOSE
5NAG24Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:200 , TYR A:453 , GLY A:454 , THR A:455 , NAG A:502 , HOH A:660 , HOH A:734BINDING SITE FOR RESIDUE NAG A 501
02AC2SOFTWAREASN A:393 , ARG A:394 , NAG A:501 , BMA A:503 , HOH A:626BINDING SITE FOR RESIDUE NAG A 502
03AC3SOFTWAREGLN A:391 , ILE A:392 , ARG A:394 , NAG A:502 , MAN A:504 , MAN A:505BINDING SITE FOR RESIDUE BMA A 503
04AC4SOFTWAREASP A:330 , GLN A:391 , BMA A:503 , HOH A:722BINDING SITE FOR RESIDUE MAN A 504
05AC5SOFTWAREILE A:392 , BMA A:503 , HOH A:695BINDING SITE FOR RESIDUE MAN A 505
06AC6SOFTWAREASN A:146 , NAG A:507BINDING SITE FOR RESIDUE NAG A 506
07AC7SOFTWARENAG A:506BINDING SITE FOR RESIDUE NAG A 507
08AC8SOFTWAREASN A:234 , HOH A:716BINDING SITE FOR RESIDUE NAG A 508
09AC9SOFTWAREASN A:367 , SER A:370 , ARG A:400BINDING SITE FOR RESIDUE NAG A 509
10BC1SOFTWAREASP A:293 , GLY A:297 , ASP A:324 , GLY A:345 , HIS A:347 , HOH A:684BINDING SITE FOR RESIDUE CA A 510
11BC2SOFTWAREARG A:118 , GLU A:119 , ASP A:151 , ARG A:152 , ARG A:224 , GLU A:276 , ARG A:292 , HIS A:347 , ARG A:371 , TYR A:406 , HOH A:728BINDING SITE FOR RESIDUE G39 A 512

(-) 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 4GZP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GZP)

(-) Exons   (0, 0)

(no "Exon" information available for 4GZP)

(-) 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
                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4gzpa_ 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.hhhh.eeeeee..eeeeeee..............eee..eeeeeeeee.....eeeeeeeee..eeeeeee........eeeeeeee..eeeeeee........eeeee......eeeee....................................eeee..eeeeee.......eeeeeeeee.........eeeeeeeeeeeeee...eeeeeee....eeeeeeeeeeee.........eeeeeeeeeee.................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gzp A  82 AEYRNWSKPQCDITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVVSWSKEILRTQESECVCINGTCTVVMTDGSASGKADTKILFIEEGKIVHTSTLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNRPIVDINIKDHSIVSSYVCSGLVGDTPRKNDSSSSSHCLDPNNEEGGHGVKGWAFDDGNDVWMGRTINETSRLGYETFKVIEGWSNPKSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINRCFYVELIRGRKEETEVLWTSNSIVVFCGTSGTYGTGSWPDGADLNLMPI 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  (0, 0)

(no "CATH Domain" information available for 4GZP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GZP)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)

 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 ]
    G39  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ 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 ]
 
  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
  4gzp
    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
  K7N5N3_9INFA | K7N5N3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  K7N5N3_9INFA | K7N5N3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        K7N5N3_9INFA | K7N5N3: 4gzo 4gzq 4gzt 4gzw 4gzx

(-) Related Entries Specified in the PDB File

4gzo 4gzq 4gzs 4gzt 4gzw 4gzx