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 :  NMR STRUCTURE OF VAT-N: THE N-TERMINAL DOMAIN OF VAT (VCP-LIKE ATPASE OF THERMOPLASMA)
 
Authors :  M. Coles, T. Diercks, J. Liermann, A. Groeger, B. Rockel, W. Baumeister K. Koretke, A. Lupas, J. Peters, H. Kessler
Date :  01 Sep 99  (Deposition) - 12 Oct 99  (Release) - 11 Aug 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Double-Psi Beta-Barrel, Beta-Clam, Substrate Recognition Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Coles, T. Diercks, J. Liermann, A. Groger, B. Rockel, W. Baumeister K. K. Koretke, A. Lupas, J. Peters, H. Kessler
The Solution Structure Of Vat-N Reveals A 'Missing Link' In The Evolution Of Complex Enzymes From A Simple Betaalphabetabeta Element.
Curr. Biol. V. 9 1158 1999
PubMed-ID: 10531028  |  Reference-DOI: 10.1016/S0960-9822(00)80017-2

(-) Compounds

Molecule 1 - VCP-LIKE ATPASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 2303

 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 1CZ4)

(-) Sites  (0, 0)

(no "Site" information available for 1CZ4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CZ4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CZ4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CZ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1CZ4)

(-) Exons   (0, 0)

(no "Exon" information available for 1CZ4)

(-) 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:185
 aligned with VAT_THEAC | O05209 from UniProtKB/Swiss-Prot  Length:745

    Alignment length:194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    
            VAT_THEAC     1 MESNNGIILRVAEANSTDPGMSRVRLDESSRRLLDAEIGDVVEIEKVRKTVGRVYRARPEDENKGIVRIDSVMRNNCGASIGDKVKVRKVRTEIAKKVTLAPIIRKDQRLKFGEGIEEYVQRALIRRPMLEQDNISVPGLTLAGQTGLLFKVVKTLPSKVPVEIGEETKIEIREEPASEVLEEVSRISYEDIGG 194
               SCOP domains d1cz4a1 A:1-91 N-terminal domain of VAT-N, VAT-Nn                                          d1cz4a2 A:92-185 C-terminal domain of VAT-N, VAT-Nc                                                     SCOP domains
               CATH domains 1cz4A01 A:1-92  [code=2.40.40.20, no name defined]                                          1cz4A02 A:93-173  [code=3.10.330.10, no name defined]                            --------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee..........eeeehhhhhhh.......eeeee...eeeeeeee.........eee.hhhhhhhhh.....eeeeeee......eeeeeee...........hhhhhhhhhhh..ee....ee.............eeeeeee......ee.....eeee...........---------.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cz4 A   1 MESNNGIILRVAEANSTDPGMSRVRLDESSRRLLDAEIGDVVEIEKVRKTVGRVYRARPEDENKGIVRIDSVMRNNCGASIGDKVKVRKVRTEIAKKVTLAPIIRKDQRLKFGEGIEEYVQRALIRRPMLEQDNISVPGLTLAGQTGLLFKVVKTLPSKVPVEIGEETKIEIREEPASEVLEE---------GG 185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  |      -  | 
                                                                                                                                                                                                                183       184
   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  (2, 2)

NMR Structure
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

NMR Structure
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CZ4)

(-) Gene Ontology  (3, 3)

NMR Structure(hide GO term definitions)
Chain A   (VAT_THEAC | O05209)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

 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 1cz4)
 
  Sites
(no "Sites" information available for 1cz4)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1cz4)
 

(-) 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
  1cz4
    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
  VAT_THEAC | O05209
    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
  VAT_THEAC | O05209
    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
        VAT_THEAC | O05209: 1cz5 5g4f 5g4g 5vc7 5vca

(-) Related Entries Specified in the PDB File

4376 CHEMICAL SHIFTS, 3JHNHA COUPLING-CONSTANTS AND HET. NOE VALUES
1cz5 ENSEMBLE OF 25 NMR STRUCTURES