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

(-) Description

Title :  STRUCTURE OF THE RESUSCITATION PROMOTING FACTOR INTERACTING PROTEIN RIPA MUTATED AT H432
 
Authors :  F. Squeglia, A. Ruggiero, M. Romano, L. Vitagliano, R. Berisio
Date :  15 Apr 14  (Deposition) - 10 Sep 14  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.38
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Squeglia, A. Ruggiero, M. Romano, L. Vitagliano, R. Berisio
Mutational And Structural Study Of Ripa, A Key Enzyme In Mycobacterium Tuberculosis Cell Division: Evidence For The L-To-D Inversion Of Configuration Of The Catalytic Cysteine
Acta Crystallogr. , Sect. D V. 70 2295 2014
PubMed-ID: 25195744  |  Reference-DOI: 10.1107/S1399004714013674

(-) Compounds

Molecule 1 - PEPTIDOGLYCAN ENDOPEPTIDASE RIPA
    Chains: A
    EC Number: 3.4.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RIPA
    Gene: RIPA, RV1477
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: MACROPHAGE INVASION AND INTRACELLULAR PERSISTENCE PROTEIN A, RESUSCITATION-PROMOTING FACTOR INTERACTION PARTNER A, RPF-INTERACTING PROTEIN A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4Q4N)

(-) Sites  (0, 0)

(no "Site" information available for 4Q4N)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q4N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Q4N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q4N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q4N)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q4N)

(-) 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:208
                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeee....eeeehhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhh................ee.hhhhh..ee.hhhhhhhhhhhh.......hhhhhhh..eeee.hhh....eeeehhhhh.eeeeeee..eeee........eeee........eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4q4n A 1003 GLWDPTLPMIPSANIPGDPIAVVNQVLGISATSAQVTANMGRKFLEQLGILQPTDTGITNAPAGSAQGRIPRVYGRQASEYVIRRGMSQIGVPYSWGGGNAAGPSKGIDSGAGTVGFDCSGLVLYSFAGVGIKLPHYSGSQYNLGRKIPSSQMRRGDVIFYGPNGSQAVTIYLGNGQMLEAPDVGLKVRVAPVRTAGMTPYVVRYIEY 1210
                                  1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202
   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 4Q4N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q4N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q4N)

(-) Gene Ontology  (10, 10)

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
(no "Ligands, Modified Residues, Ions" information available for 4q4n)
 
  Sites
(no "Sites" information available for 4q4n)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4q4n)
 

(-) 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 ](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
  4q4n
    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
  RIPA_MYCTU | O53168
    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)
  3.4.-.-
    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
  RIPA_MYCTU | O53168
    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
        RIPA_MYCTU | O53168: 2xiv 3ne0 3pbc 3s0q 4q4g 4q4t

(-) Related Entries Specified in the PDB File

4q4g 4q4t