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

(-) Description

Title :  INFLUENZA POLYMERASE BASIC PROTEIN 2 (PB2) BOUND TO A SMALL-MOLECULE INHIBITOR
 
Authors :  M. D. Jacobs
Date :  24 Oct 13  (Deposition) - 30 Jul 14  (Release) - 27 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.82
Chains :  Asym./Biol. Unit :  A
Keywords :  Rna-Dependent Rna Polymerase, Transcription, Pb2 Subunit, Influenza Virus, Cap-Binding Domain, Transcription-Transcription Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. P. Clark, M. W. Ledeboer, I. Davies, R. A. Byrn, S. M. Jones, E. Perola A. Tsai, M. Jacobs, K. Nti-Addae, U. K. Bandarage, M. J. Boyd, R. S. Bethiel, J. J. Court, H. Deng, J. P. Duffy, W. A. Dorsch, L. J. Farmer, H. Gao, W. Gu, K. Jackson, D. H. Jacobs, J. M. Kennedy, B. Ledford, J. Liang, F. Maltais, M. Murcko, T. Wang, M. W. Wannamaker, H. B. Bennett, J. R. Leeman, C. Mcneil, W. P. Taylor, C. Memmott, M. Jiang, R. Rijnbrand, C. Bral, U. Germann, A. Nezami, Y. Zhang, F. G. Salituro, Y. L. Bennani, P. S. Charifson
Discovery Of A Novel, First-In-Class, Orally Bioavailable Azaindole Inhibitor (Vx-787) Of Influenza Pb2.
J. Med. Chem. V. 57 6668 2014
PubMed-ID: 25019388  |  Reference-DOI: 10.1021/JM5007275

(-) Compounds

Molecule 1 - POLYMERASE BASIC PROTEIN 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B.1
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CAP-BINDING DOMAIN
    Gene: PB2, POLYMERASE BASIC PROTEIN 2 PB2
    Mutation: YES
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 392809
    Strain: A/VICTORIA/3/1975 H3N2
    Synonym: RNA-DIRECTED RNA POLYMERASE SUBUNIT P3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
17041Ligand/IonN~2~-[2-(5-CHLORO-1H-PYRROLO[2,3-B]PYRIDIN-3-YL)-5-FLUOROPYRIMIDIN-4-YL]-N,N-DIMETHYL-L-ALANINAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:323 , SER A:324 , PHE A:325 , SER A:337 , HIS A:357 , GLU A:361 , LYS A:376 , PHE A:404 , MET A:431BINDING SITE FOR RESIDUE 704 A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NCM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NCM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NCM)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NCM)

(-) Sequences/Alignments

Asymmetric/Biological 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:163
                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeeeeee..eeeeeeee.....eeeeeeee..eeeeee...eeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhh.hhhhhh.........hhhhh..hhhhhhhhhhhhhhhhhhhhhheee......eeee.....ee..eee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ncm A 321 SSFSFGGFTFKRTSGSSIKREEEVLTGNLQTLKIRVHEGYEEFTMVGKRATAILRKATRRLVQLIVSGKDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEHIDNVMGMVGVLPDMTPSTEMSMRGIRVSKM 483
                                   330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480
   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 4NCM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    704  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ncm)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  4ncm
    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
  PB2_I75A3 | P31345
    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)
  (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
  PB2_I75A3 | P31345
    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
        PB2_I75A3 | P31345: 2gmo 2jdq 2vqz 2vy6 2vy7 2vy8 4nce 4p1u 4uad 4uae 4uaf

(-) Related Entries Specified in the PDB File

4nce