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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE FIRST NUCLEOTIDE BINDING DOMAIN OF CHAPERONE CLPB1, PUTATIVE, (PV089580) FROM PLASMODIUM VIVAX
 
Authors :  A. K. Wernimont, J. Lew, I. Kozieradzki, Y. H. Lin, A. Hassanali, Y. Zhao, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, M. Sundstrom, A. Bochkarev, R. Hui, J. D. Artz, Structural Genomics Consortium (Sgc)
Date :  16 Mar 07  (Deposition) - 03 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Clpb, Plasmodium, Malaria, Structural Genomics, Structural Genomics Consortium, Sgc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Wernimont, J. Lew, I. Kozieradzki, Y. H. Lin, A. Hassanali, Y. Zhao, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, M. Sundstrom, A. Bochkarev, R. Hui, J. D. Artz
Crystal Structure Of The First Nucleotide Binding Domain Of Chaperone Clpb1, Putative, (Pv089580) From Plasmodium Vivax
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN PF08_0063
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15-TEV-LIC
    Expression System Strain: ROSETTA-OXFORD
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PUTATIVE NUCLEOTIDE BINDING DOMAIN (RESIDUES 190- 480)
    Organism Common: MALARIA PARASITE P. FALCIPARUM
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2P65)

(-) Sites  (0, 0)

(no "Site" information available for 2P65)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P65)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:3 -Ala A:4

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P65)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P65)

(-) Exons   (0, 0)

(no "Exon" information available for 2P65)

(-) 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:185
 aligned with Q8IB03_PLAF7 | Q8IB03 from UniProtKB/TrEMBL  Length:1070

    Alignment length:185
                                   321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491     
         Q8IB03_PLAF7   312 QALEKYSRDLTALARAGKLDPVIGRDNEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLVSLDMSSLIAGAKYRGDFEERLKSILKEVQDAEGQVVMFIDEIHTVVGAGAVAEGALDAGNILKPMLARGELRCIGATTVSEYRQFIEKDKALERRFQQILVEQPS 496
               SCOP domains d2p65a_ A: automated matches                                                                                                                                                              SCOP domains
               CATH domains 2p65A00 A:3-187 P-loop containing nucleotide triphosphate hydrolases                                                                                                                      CATH domains
               Pfam domains -------------------------------------------AAA-2p65A01 A:46-184                                                                                                                       --- Pfam domains
         Sec.struct. author ......eeehhhhhhh........hhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhh..........eeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeeee.hhhhhh...........hhhhhhhhhhh....eeeeehhhhhhhhh..hhhhhhheeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p65 A   3 QALEKYSRDLTALARAGKLDPVIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLVSLDLSSLIAGAKYRGDFEERLKSILKEVQDAEGQVVMFIDEIHTVVGAGAVAEGALDAGNILKPMLARGELRCIGATTVSEYRQFIEKDKALERRFQQILVEQPS 187
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182
   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)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8IB03_PLAF7 | Q8IB03)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    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.
biological process
    GO:0019538    protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.
cellular component
    GO:0020011    apicoplast    The plastid organelle found in apicomplexans.

 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
(no "Ligands, Modified Residues, Ions" information available for 2p65)
 
  Sites
(no "Sites" information available for 2p65)
 
  Cis Peptide Bonds
    Gln A:3 - Ala A:4   [ 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 ](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
  2p65
    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
  Q8IB03_PLAF7 | Q8IB03
    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
  Q8IB03_PLAF7 | Q8IB03
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8IB03_PLAF7 | Q8IB03: 4xbi

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2P65)