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
(-)Biological Unit 2
(-)Biological Unit 3
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  THE 1.35A STRUCTURE OF A VIRAL RNASE L ANTAGONIST REVEALS BASIS FOR THE 2'-5'-OLIGOADENYLATE BINDING AND ENZYME ACTIVITY.
 
Authors :  L. Hu, B. V. V. Prasad
Date :  31 Oct 14  (Deposition) - 29 Apr 15  (Release) - 19 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  2H Phosphodiesterase, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Ogden, L. Hu, B. K. Jha, B. Sankaran, S. R. Weiss, R. H. Silverman, J. T. Patton, B. V. Prasad
Structural Basis For 2'-5'-Oligoadenylate Binding And Enzym Activity Of A Viral Rnase L Antagonist.
J. Virol. V. 89 6633 2015
PubMed-ID: 25878106  |  Reference-DOI: 10.1128/JVI.00701-15

(-) Compounds

Molecule 1 - CAPPING ENZYME PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: C-TERMINAL DOMAIN, UNP RESIDUES 694-835
    Organism Scientific: ROTAVIRUS A
    Organism Taxid: 28875
    Strain: RRV
    Synonym: CAPPING PROTEIN VP3, VP3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MLI2Ligand/IonMALONATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MLI1Ligand/IonMALONATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MLI1Ligand/IonMALONATE ION
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MLI2Ligand/IonMALONATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:767 , SER A:768 , GLY A:769 , VAL A:770 , LEU A:771 , ILE A:795 , PRO A:796 , HOH A:1128 , HOH A:1153 , TYR B:754BINDING SITE FOR RESIDUE MLI A 1001
2AC2SOFTWAREPHE A:700 , HIS A:718 , THR A:720 , HOH A:1187BINDING SITE FOR RESIDUE EDO A 1002
3AC3SOFTWARETYR A:754 , VAL B:767 , SER B:768 , GLY B:769 , VAL B:770 , LEU B:771 , ILE B:795 , PRO B:796 , HOH B:1122 , HOH B:1161BINDING SITE FOR RESIDUE MLI B 1001
4AC4SOFTWAREHIS B:718 , THR B:720 , HOH B:1238BINDING SITE FOR RESIDUE EDO B 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RPT)

(-) 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:144
                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeee.............eeeeeee.hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeee....hhhhhhhhhhhhhhh..ee........eeeee.......eeeeee..eeeeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rpt A 692 SGADDPNYFIGIKFRHIPYEYDVKIPHLTFGVLFISDNMIPDVVEIMKIMKKELFEMDITTSYTYMLSDGIYVANVSGVLATYFKMYNLFYKSQITFGQSRMFIPHITLSFSNNKTVRIESTRLKISSIYLRKIKGDTVFDMSE 835
                                   701       711       721       731       741       751       761       771       781       791       801       811       821       831    


Chain B from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.............eeeeeee.hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeee....hhhhhhhhhhhhhhh..ee........eeeee.......eeeeee..eeeeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rpt B 696 DPNYFIGIKFRHIPYEYDVKIPHLTFGVLFISDNMIPDVVEIMKIMKKELFEMDITTSYTYMLSDGIYVANVSGVLATYFKMYNLFYKSQITFGQSRMFIPHITLSFSNNKTVRIESTRLKISSIYLRKIKGDTVFDMSE 835
                                   705       715       725       735       745       755       765       775       785       795       805       815       825       835
   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 4RPT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MLI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4rpt)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 2 PNG format | Biol. Unit 3 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
  4rpt
    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
  B3F2X4_9REOV | B3F2X4
    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
  B3F2X4_9REOV | B3F2X4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B3F2X4_9REOV | B3F2X4: 4ye2

(-) Related Entries Specified in the PDB File

4ye2