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

(-) Description

Title :  CLPB NBD2 FROM T. THERMOPHILUS, NUCLEOTIDE-FREE
 
Authors :  C. Zeymer, T. R. M. Barends, N. D. Werbeck, I. Schlichting, J. Reinstein
Date :  04 Jul 13  (Deposition) - 12 Feb 14  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Aaa+ Protein, Nucleotide Binding Domain, Molecular Chaperone, Disaggregase, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Zeymer, T. R. M. Barends, N. D. Werbeck, I. Schlichting, J. Reinstei
Elements In Nucleotide Sensing And Hydrolysis Of The Aaa+ Disaggregation Machine Clpb: A Structure-Based Mechanistic Dissection Of A Molecular Motor
Acta Crystallogr. , Sect. D V. 70 582 2014
PubMed-ID: 24531492  |  Reference-DOI: 10.1107/S1399004713030629

(-) Compounds

Molecule 1 - CHAPERONE PROTEIN CLPB
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3) RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentNUCLEOTIDE BINDING DOMAIN 2, UNP RESIDUES 520-854
    GeneCLPB
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid300852
    StrainHB8

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:598 , VAL A:599 , GLY A:600 , LYS A:601 , THR A:602 , GLU A:603 , ARG A:806BINDING SITE FOR RESIDUE PO4 A 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LJ4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LJ4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LJ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LJ4)

(-) Exons   (0, 0)

(no "Exon" information available for 4LJ4)

(-) 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:319
                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.........eeeeee.....hhhhhhhhhhhhhh.hhh.eeeee.hhh...hhhhhhh.hhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhheee.....eee....eeeee...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......eeeeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lj4 A 518 HMEVTEEDIAEIVSRWTGIPVSKLLEGEEKLLRLEEELHKRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLIGQLTEAVRRRPYSVILFDEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIVEIQLSYLRARLAEKRISLELTEAAKDFLAERGYDPVFGARPLRRVIQRELETPLAQKILAGEVKEGDRVQVDVGPAGLVFAVP 849
                                   527       537       548       558       568       578       588       598       608       618       628       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840         
                                                     545|                                                                                       637|                                                                                                                                                                                                       
                                                      547                                                                                        650                                                                                                                                                                                                       

   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 4LJ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LJ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LJ4)

(-) Gene Ontology  (8, 8)

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
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4lj4)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4lj4
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CLPB_THET8 | Q9RA63
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CLPB_THET8 | Q9RA63
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CLPB_THET8 | Q9RA631qvr 4fct 4fcv 4fcw 4fd2 4hse 4lj5 4lj6 4lj7 4lj8 4lj9 4lja

(-) Related Entries Specified in the PDB File

4lj5 4lj6 4lj7 4lj8 4lj9 4lja