Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE TRANS-EDITING ENZYME FOR PROLYL TRNA SYNTHETASE
 
Authors :  K. Murayama, N. Nakagawa, A. Ebihara, S. Kuramitsu, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 Jun 05  (Deposition) - 28 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Trans-Editing Domain, Prolyl-Trna Synthetase, Rsgi, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Murayama, N. Nakagawa, A. Ebihara, S. Kuramitsu, M. Shirouzu, S. Yokoyama
Crystal Structure Of A Putative Trans-Editing Enzyme For Prolyl Trna Synthetase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - A PUTATIVE TRANS-EDITING ENZYME
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2CX5)

(-) Sites  (0, 0)

(no "Site" information available for 2CX5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CX5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CX5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CX5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CX5)

(-) Exons   (0, 0)

(no "Exon" information available for 2CX5)

(-) 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:157
 aligned with Q5SHN1_THET8 | Q5SHN1 from UniProtKB/TrEMBL  Length:158

    Alignment length:157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       
         Q5SHN1_THET8     2 SLSPSARRVQGALETRGFGHLKVVELPASTRTAKEAAQAVGAEVGQIVKSLVFVGEKGAYLFLVSGKNRLDLGKATRLVGGPLRQATPEEVRELTGFAIGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEG 158
               SCOP domains d2cx5a_ A: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh......eee......hhhhhhhhhh.hhh.eeeeeeee....eeeeeee.....hhhhhhhhhh...ee.hhhhhhhhhh................eeee.hhhhh..eeee.....eeeeehhhhhhhhhh.eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cx5 A   2 SLSPSARRVQGALETRGFGHLKVVELPASTRTAKEAAQAVGAEVGQIVKSLVFVGEKGAYLFLVSGKNRLDLGKATRLVGGPLRQATPEEVRELTGFAIGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEG 158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       


Chain B from PDB  Type:PROTEIN  Length:157
 aligned with Q5SHN1_THET8 | Q5SHN1 from UniProtKB/TrEMBL  Length:158

    Alignment length:157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       
         Q5SHN1_THET8     2 SLSPSARRVQGALETRGFGHLKVVELPASTRTAKEAAQAVGAEVGQIVKSLVFVGEKGAYLFLVSGKNRLDLGKATRLVGGPLRQATPEEVRELTGFAIGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEG 158
               SCOP domains d2cx5b_ B: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.....eee......hhhhhhhhhh.hhhh.eeeeeeee...eeeeeee.....hhhhhhhhhh..eee.hhhhhhhhhh................eeee.hhhhh..eeee.....eeeeehhhhhhhhhh.eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cx5 B   2 SLSPSARRVQGALETRGFGHLKVVELPASTRTAKEAAQAVGAEVGQIVKSLVFVGEKGAYLFLVSGKNRLDLGKATRLVGGPLRQATPEEVRELTGFAIGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEG 158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       


Chain C from PDB  Type:PROTEIN  Length:157
 aligned with Q5SHN1_THET8 | Q5SHN1 from UniProtKB/TrEMBL  Length:158

    Alignment length:157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       
         Q5SHN1_THET8     2 SLSPSARRVQGALETRGFGHLKVVELPASTRTAKEAAQAVGAEVGQIVKSLVFVGEKGAYLFLVSGKNRLDLGKATRLVGGPLRQATPEEVRELTGFAIGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEG 158
               SCOP domains d2cx5c_ C: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.....eee......hhhhhhhhhh.hhh.eeeeeeee....eeeeeee.....hhhhhhhhhh...ee.hhhhhhhhhh................eeee.hhhhh..eeee.....eeeeehhhhhhhhhh.eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cx5 C   2 SLSPSARRVQGALETRGFGHLKVVELPASTRTAKEAAQAVGAEVGQIVKSLVFVGEKGAYLFLVSGKNRLDLGKATRLVGGPLRQATPEEVRELTGFAIGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEG 158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       


Chain D from PDB  Type:PROTEIN  Length:157
 aligned with Q5SHN1_THET8 | Q5SHN1 from UniProtKB/TrEMBL  Length:158

    Alignment length:157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       
         Q5SHN1_THET8     2 SLSPSARRVQGALETRGFGHLKVVELPASTRTAKEAAQAVGAEVGQIVKSLVFVGEKGAYLFLVSGKNRLDLGKATRLVGGPLRQATPEEVRELTGFAIGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEG 158
               SCOP domains d2cx5d_ D: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh......eee......hhhhhhhhh..hhh.eeeeeeeee...eeeeeee.....hhhhhhhhhh..eee.hhhhhhhhhh................eeee.hhhhh..eeee.....eeeeehhhhhhhhhh.eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cx5 D   2 SLSPSARRVQGALETRGFGHLKVVELPASTRTAKEAAQAVGAEVGQIVKSLVFVGEKGAYLFLVSGKNRLDLGKATRLVGGPLRQATPEEVRELTGFAIGGVPPVGHNTPLPAYLDEDLLGYPEVWAAGGTPRALFRATPKELLALTGAQVADLKEG 158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CX5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CX5)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q5SHN1_THET8 | Q5SHN1)
molecular function
    GO:0002161    aminoacyl-tRNA editing activity    The hydrolysis of an incorrectly aminoacylated tRNA.
biological process
    GO:0006450    regulation of translational fidelity    Any process that modulates the ability of the translational apparatus to interpret the genetic code.

 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
(no "Ligands, Modified Residues, Ions" information available for 2cx5)
 
  Sites
(no "Sites" information available for 2cx5)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2cx5)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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 | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 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
  2cx5
    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
  Q5SHN1_THET8 | Q5SHN1
    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
  Q5SHN1_THET8 | Q5SHN1
    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
        Q5SHN1_THET8 | Q5SHN1: 3ri0 3rij
UniProtKB/TrEMBL
        Q5SHN1_THET8 | Q5SHN1: 2z0k 2z0x

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2CX5)