Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  THE SOLUTION STRUCTURE OF THE ARCHAEGLOBUS FULGIDIS PROTEIN AF2095. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET GR4
 
Authors :  R. Powers, T. B. Acton, Y. J. Huang, J. Liu, L. Ma, B. Rost, Y. Chiang, J. R. Cort, M. A. Kennedy, G. T. Montelione, Northeast Structural Genomics Consortium (Nesg)
Date :  29 Dec 03  (Deposition) - 16 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Beta-Sheet Of 4 Parallel, Anti-Parallel Beta-Strands And 3 Alpha-Helices, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Powers, N. Mirkovic, S. Goldsmith-Fischman, T. B. Acton, Y. Chiang, Y. J. Huang, L. Ma, P. K. Rajan, J. R. Cort, M. A. Kennedy, J. Liu, B. Rost, B. Honig, D. Murray, G. T. Montelione
Solution Structure Of Archaeglobus Fulgidis Peptidyl-Trna Hydrolase (Pth2) Provides Evidence For An Extensive Conserved Family Of Pth2 Enzymes In Archea, Bacteria, And Eukaryotes
Protein Sci. V. 14 2849 2005
PubMed-ID: 16251366  |  Reference-DOI: 10.1110/PS.051666705
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN AF2095(GR4)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)+ MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AF2095
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1RZW)

(-) Sites  (0, 0)

(no "Site" information available for 1RZW)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RZW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RZW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RZW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RZW)

(-) Exons   (0, 0)

(no "Exon" information available for 1RZW)

(-) Sequences/Alignments

NMR Structure
   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:123
 aligned with PTH_ARCFU | O28185 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:123
                                                                                                                                            115        
                                    10        20        30        40        50        60        70        80        90       100       110    |    -   
            PTH_ARCFU     1 MTLKQVIVVRDDLKLSRGKLAVQVAHAAIIGYLKSDSSLRRKWLDEGQKKVVLKVKSLEELLGIKHKAESLGLVTGLVQDAGLTEVPPGTITAVVIGPDEERKIDKVTGNLPLLK--------   -
               SCOP domains d1rzwa_ A: Hypothetical protein AF2095                                                                                      SCOP domains
               CATH domains 1rzwA01 A:1-114 Bit1                                                                                              --------- CATH domains
               Pfam domains -PTH2-1rzwA01 A:2-114                                                                                             --------- Pfam domains
         Sec.struct. author ...eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh...eeee.............eeeeeeeehhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rzw A   1 MTLKQVIVVRDDLKLSRGKLAVQVAHAAIIGYLKSDSSLRRKWLDEGQKKVVLKVKSLEELLGIKHKAESLGLVTGLVQDAGLTEVPPGTITAVVIGPDEERKIDKVTGNLPLLKLEHHHHHH 123
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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, 1)

NMR Structure
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: PTH2 (5)

(-) Gene Ontology  (4, 4)

NMR Structure(hide GO term definitions)
Chain A   (PTH_ARCFU | O28185)
molecular function
    GO:0004045    aminoacyl-tRNA hydrolase activity    Catalysis of the reaction: N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

NMR Structure
  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 1rzw)
 
  Sites
(no "Sites" information available for 1rzw)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1rzw)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models 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
  1rzw
    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
  PTH_ARCFU | O28185
    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
  PTH_ARCFU | O28185
    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
        PTH_ARCFU | O28185: 3erj

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1RZW)