Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION NMR STRUCTURE OF THE INFLUENZA A VIRUS S31N MUTANT (19-49) IN PRESENCE OF DRUG M2WJ332
 
Authors :  Y. Wu, J. Wang, W. Degrado
Date :  10 Sep 12  (Deposition) - 09 Jan 13  (Release) - 06 Feb 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C,D  (20x)
NMR Structure *:  A,B,C,D  (1x)
Keywords :  Influenza A Virus, M2 Channel, S31N Inhibitor, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Wang, Y. Wu, C. Ma, G. Fiorin, J. Wang, L. H. Pinto, R. A. Lamb, M. L. Klein, W. F. Degrado
Structure And Inhibition Of The Drug-Resistant S31N Mutant Of The M2 Ion Channel Of Influenza A Virus.
Proc. Natl. Acad. Sci. Usa V. 110 1315 2013
PubMed-ID: 23302696  |  Reference-DOI: 10.1073/PNAS.1216526110

(-) Compounds

Molecule 1 - MEMBRANE ION CHANNEL M2
    Chains: A, B, C, D
    Engineered: YES
    Mutation: YES
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 221020
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
NMR Structure (20x): ABCD
NMR Structure * (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1A2Y1Ligand/Ion(3S,5S,7S)-N-{[5-(THIOPHEN-2-YL)-1,2-OXAZOL-3-YL]METHYL}TRICYCLO[3.3.1.1~3,7~]DECAN-1-AMINIUM
NMR Structure * (1, 1)
No.NameCountTypeFull Name
1A2Y1Ligand/Ion(3S,5S,7S)-N-{[5-(THIOPHEN-2-YL)-1,2-OXAZOL-3-YL]METHYL}TRICYCLO[3.3.1.1~3,7~]DECAN-1-AMINIUM

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:27 , ALA A:30 , VAL B:27 , VAL C:27 , VAL D:27BINDING SITE FOR RESIDUE A2Y A 100

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2LY0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2LY0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2LY0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2LY0)

(-) Exons   (0, 0)

(no "Exon" information available for 2LY0)

(-) Sequences/Alignments

NMR Structure
   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:31
 aligned with Q6XT21_9INFA | Q6XT21 from UniProtKB/TrEMBL  Length:97

    Alignment length:31
                                    28        38        48 
          Q6XT21_9INFA   19 CNDSSDPLVVAANIIGILHLILWILDRLFFK 49
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                  2ly0 A 19 SNDSSDPLVVAANIIGILHLILWILDRLFFK 49
                                    28        38        48 


Chain B from PDB  Type:PROTEIN  Length:31
 aligned with Q6XT21_9INFA | Q6XT21 from UniProtKB/TrEMBL  Length:97

    Alignment length:31
                                    28        38        48 
          Q6XT21_9INFA   19 CNDSSDPLVVAANIIGILHLILWILDRLFFK 49
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                  2ly0 B 19 SNDSSDPLVVAANIIGILHLILWILDRLFFK 49
                                    28        38        48 


Chain C from PDB  Type:PROTEIN  Length:31
 aligned with Q6XT21_9INFA | Q6XT21 from UniProtKB/TrEMBL  Length:97

    Alignment length:31
                                    28        38        48 
          Q6XT21_9INFA   19 CNDSSDPLVVAANIIGILHLILWILDRLFFK 49
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                  2ly0 C 19 SNDSSDPLVVAANIIGILHLILWILDRLFFK 49
                                    28        38        48 


Chain D from PDB  Type:PROTEIN  Length:31
 aligned with Q6XT21_9INFA | Q6XT21 from UniProtKB/TrEMBL  Length:97

    Alignment length:31
                                    28        38        48 
          Q6XT21_9INFA   19 CNDSSDPLVVAANIIGILHLILWILDRLFFK 49
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                  2ly0 D 19 SNDSSDPLVVAANIIGILHLILWILDRLFFK 49
                                    28        38        48
   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  (0, 0)

(no "SCOP Domain" information available for 2LY0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2LY0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2LY0)

(-) Gene Ontology  (13, 13)

NMR Structure(hide GO term definitions)
Chain A,B,C,D   (Q6XT21_9INFA | Q6XT21)
molecular function
    GO:0015078    hydrogen ion transmembrane transporter activity    Enables the transfer of hydrogen ions from one side of a membrane to the other.
biological process
    GO:1902600    hydrogen ion transmembrane transport    The directed movement of hydrogen ion (proton) across a membrane.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0015992    proton transport    The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0039521    suppression by virus of host autophagy    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of autophagy in the host.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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

NMR Structure
  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
    A2Y  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ly0)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - model 1, sites PNG format | NMR Structure - all models 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
  2ly0
    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
  Q6XT21_9INFA | Q6XT21
    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
  Q6XT21_9INFA | Q6XT21
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2LY0)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2LY0)