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 :  LASSA VIRUS L PROTEIN CAP-SNATCHING ENDONUCLEASE. BOUND TO TWO MANGANESE IONS
 
Authors :  J. Reguera, S. Cusack
Date :  29 Mar 16  (Deposition) - 29 Jun 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.36
Chains :  Asym./Biol. Unit :  A
Keywords :  Cap-Snatching Nuclease Lassa Transcription, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Reguera, P. Gerlach, M. Rosenthal, S. Gaudon, F. Coscia, S. Gunther S. Cusack
Comparative Structural And Functional Analysis Of Bunyaviru And Arenavirus Cap-Snatching Endonucleases.
Plos Pathog. V. 12 05636 2016
PubMed-ID: 27304209  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1005636

(-) Compounds

Molecule 1 - RNA-DIRECTED RNA POLYMERASE L
    Chains: A
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Taxid: 83333
    Organism Scientific: LASSA MAMMARENAVIRUS
    Organism Taxid: 11620
    Synonym: PROTEIN L

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1MN33Ligand/IonMANGANESE (III) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:3 , GLU A:51 , ASP A:89 , MN3 A:202binding site for residue MN3 A 201
2AC2SOFTWAREASP A:89 , GLU A:102 , MN3 A:201 , HOH A:303binding site for residue MN3 A 202
3AC3SOFTWAREHIS A:76 , HOH A:301 , HOH A:313binding site for residue MN3 A 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J1P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5J1P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J1P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J1P)

(-) Exons   (0, 0)

(no "Exon" information available for 5J1P)

(-) 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:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..ee.....hhhhhhhhh...........eeeee..eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j1p A   0 GMEEDIACVKDLVSKYLADNERLSRQKLAFLVQTEPRMLLMEGLKLLSLCIEIDSCNANGCEHNSEDKSVERILHDHGILTLCFVVPDGYKLTGNVLILLECFVRSSPANFEQKYIEDFKKLEQLKEDLKTVNISLIPLIDGRTSFYNEQIPDWVNDKLRDTLFSLLRY 170
                                     9        19        29        39        49        59        69        79||      91       101       111       121       131       141       151       161         
                                                                                                           80|                                                                                       
                                                                                                            83
   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 5J1P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J1P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J1P)

(-) Gene Ontology  (9, 9)

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
    MN3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5j1p)
 

(-) 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
  5j1p
    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
  Q6GWS6_9VIRU | Q6GWS6
    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)
  2.7.7.48
    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
  Q6GWS6_9VIRU | Q6GWS6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q6GWS6_9VIRU | Q6GWS6: 5izh 5j1n

(-) Related Entries Specified in the PDB File

5ize 5izh 5j1n