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 :  CRYSTAL STRUCTURE OF CLPB NBD1 IN COMPLEX WITH GUANIDINIUM CHLORIDE AND ADP
 
Authors :  C. Zeymer, N. D. Werbeck, I. Schlichting, J. Reinstein
Date :  30 Oct 12  (Deposition) - 30 Jan 13  (Release) - 03 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Nucleotide Binding Domain, Aaa+ Protein, Molecular Chaperone, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Zeymer, N. D. Werbeck, I. Schlichting, J. Reinstein
The Molecular Mechanism Of Hsp100 Chaperone Inhibition By The Prion Curing Agent Guanidinium Chloride.
J. Biol. Chem. V. 288 7065 2013
PubMed-ID: 23341453  |  Reference-DOI: 10.1074/JBC.M112.432583

(-) Compounds

Molecule 1 - CHAPERONE PROTEIN CLPB
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PET28A
    Fragment: CLPB NBD1-M (141-534)
    Gene: CLPB, TTHA1487
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CL1Ligand/IonCHLORIDE ION
3GAI1Ligand/IonGUANIDINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:170 , PRO A:171 , VAL A:172 , GLU A:209 , ADP A:602BINDING SITE FOR RESIDUE GAI A 601
2AC2SOFTWAREPRO A:171 , VAL A:172 , ILE A:173 , ARG A:175 , GLY A:201 , VAL A:202 , GLY A:203 , LYS A:204 , THR A:205 , ALA A:206 , ILE A:340 , LEU A:344 , PRO A:378 , ASP A:379 , ILE A:382 , GAI A:601 , HOH A:701 , HOH A:702 , HOH A:736 , HOH A:739BINDING SITE FOR RESIDUE ADP A 602
3AC3SOFTWAREARG A:180 , ARG A:214 , GLY A:495BINDING SITE FOR RESIDUE CL A 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:377 -Pro A:378

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HSE)

(-) 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:369
                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhheeehhhhhhh........hhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhh..hhhhh..eeeeehhhhhhh.....hhhhhhhhhhhhhhhhh...eeeee.hhhhh.....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hse A 151 NALEQYGIDLTRLAAEGKLDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAVDAGNMLKPALARGELRLIGATTLDEYREIEKDPALERRFQPVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHRYITERRLPDKAIDLIDEAAARLRMALESAPEEIDALERKKLQLEIEREALSQERLKAIEAEIAKLTEEIAKLRAEWEREREILRKLREAQHRLDEVRREIELAERQYDLNRAAELRYGELPKLEAEVEALSEKLRGARFVRLEVTEEDIAEIVSR 532
                                   160       170       180       190       200       210       220       230       240       250       260       270       286       296       306       316       326       336       346       356       366       376       386       396       406       416   ||  433       443       453       463       473       483       493       503       513       523         
                                                                                                                                                         278|                                                                                                                                    420|                                                                                                        
                                                                                                                                                          285                                                                                                                                     428
   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 4HSE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GAI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:377 - Pro A:378   [ RasMol ]  
 

(-) 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 | Asym./Biol. Unit - sites 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
  4hse
    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
  CLPB_THET8 | Q9RA63
    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
  CLPB_THET8 | Q9RA63
    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
        CLPB_THET8 | Q9RA63: 1qvr 4fct 4fcv 4fcw 4fd2 4lj4 4lj5 4lj6 4lj7 4lj8 4lj9 4lja

(-) Related Entries Specified in the PDB File

1jbk 1qvr