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 :  MIDDLE DOMAIN OF PLASMODIUM FALCIPARUM PUTATIVE HEAT SHOCK PROTEIN PF14_0417
 
Authors :  V. V. Lunin, E. Botchkareva, P. Loppnau, M. Amani, J. Bray, M. Vedadi, A. C. Arrowsmith, M. Sundstrom, A. Bochkarev, R. Hui, O. Plotnikova, Str Genomics Consortium (Sgc)
Date :  07 Dec 04  (Deposition) - 08 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Heat Shock, Chaperone, Structural Genomics, Structural Genomics Consortium, Sgc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Vedadi, J. Lew, J. Artz, M. Amani, Y. Zhao, A. Dong, G. A. Wasney, M. Gao, T. Hills, S. Brokx, W. Qiu, S. Sharma, A. Diassiti, Z. Alam, M. Melone, A. Mulichak, A. Wernimont, J. Bray, P. Loppnau, O. Plotnikova, K. Newberry, E. Sundararajan, S. Houston, J. Walker, W. Tempel, A. Bochkarev, I. Kozieradzki, A. Edwards, C. Arrowsmith, D. Roos, K. Kain, R. Hui
Genome-Scale Protein Expression And Structural Biology Of Plasmodium Falciparum And Related Apicomplexan Organisms.
Mol. Biochem. Parasitol. V. 151 100 2007
PubMed-ID: 17125854  |  Reference-DOI: 10.1016/J.MOLBIOPARA.2006.10.011

(-) Compounds

Molecule 1 - HEAT SHOCK PROTEIN, PUTATIVE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11-TEV
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1Y6Z)

(-) Sites  (0, 0)

(no "Site" information available for 1Y6Z)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y6Z)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln B:42 -Ile B:43

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y6Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y6Z)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y6Z)

(-) 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:242
 aligned with Q8IL32_PLAF7 | Q8IL32 from UniProtKB/TrEMBL  Length:927

    Alignment length:258
                                   396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636        
         Q8IL32_PLAF7   387 PIWKQDEKSLTENDYYSFYKNTFKAYDDPLAYVHFNVEGQISFNSILYIPGSLPWELSKNMFDEESRGIRLYVKRVFINDKFSESIPRWLTFLRGIVDSENLPLNVGREILQKSKMLSIINKRIVLKSISMMKGLKETGGDKWTKFLNTFGKYLKIGVVEDKENQEEIASLVEFYSINSGDKKTDLDSYIENMKEDQKCIYYISGENKKTAQNSPSLEKLKALNYDVLFSLEPIDEFCLSSLTVNKYKGYEVLDVNKA 644
               SCOP domains d1y6za_ A: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh.....hhhhhhhhhhhhhh......eeeeeeee...eeeeeeee....hhhhhhh..----..eeeee..ee...hhhhhhhhhhh..eeeeee..------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..ee.........eehhhhhhh.......eeeee..hhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhh.....eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y6z A   3 PIWKQDEKSLTENDYYSFYKNTFKAYDDPLAYVHFNVEGQISFNSILYIPGSLPWELSKNMF----RGIRLYVKRVFINDKFSESIPRWLTFLRGIVDSEN------------SKMLSIINKRIVLKSISMMKGLKETGGDKWTKFLNTFGKYLKIGVVEDKENQEEIASLVEFYSINSGDKKTDLDSYIENMKEDQKCIYYISGENKKTAQNSPSLEKLKALNYDVLFSLEPIDEFCLSSLTVNKYKGYEVLDVNKA 260
                                    12        22        32        42        52        62 |    | 72        82        92       102|        -   |   122       132       142       152       162       172       182       192       202       212       222       232       242       252        
                                                                                        64   69                               103          116                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:246
 aligned with Q8IL32_PLAF7 | Q8IL32 from UniProtKB/TrEMBL  Length:927

    Alignment length:257
                                   395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       
         Q8IL32_PLAF7   386 LPIWKQDEKSLTENDYYSFYKNTFKAYDDPLAYVHFNVEGQISFNSILYIPGSLPWELSKNMFDEESRGIRLYVKRVFINDKFSESIPRWLTFLRGIVDSENLPLNVGREILQKSKMLSIINKRIVLKSISMMKGLKETGGDKWTKFLNTFGKYLKIGVVEDKENQEEIASLVEFYSINSGDKKTDLDSYIENMKEDQKCIYYISGENKKTAQNSPSLEKLKALNYDVLFSLEPIDEFCLSSLTVNKYKGYEVLDVN 642
               SCOP domains d1y6zb_ B: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.....hhhhhhhhhhhhhh......eeeeeee.....eeeeeee....hhhhh..........eeeee..eeee.hhhhhhhhhhh..eeeeee..-----------...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..ee.........eehhhhhhh.......eeeee..hhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhh.....eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y6z B   2 LPIWKQDEKSLTENDYYSFYKNTFKAYDDPLAYVHFNVEGQISFNSILYIPGSLPWELSKNMFDEESRGIRLYVKRVFINDKFSESIPRWLTFLRGIVDSEN-----------KSKMLSIINKRIVLKSISMMKGLKETGGDKWTKFLNTFGKYLKIGVVEDKENQEEIASLVEFYSINSGDKKTDLDSYIENMKEDQKCIYYISGENKKTAQNSPSLEKLKALNYDVLFSLEPIDEFCLSSLTVNKYKGYEVLDVN 258
                                    11        21        31        41        51        61        71        81        91       101 |       -   |   121       131       141       151       161       171       181       191       201       211       221       231       241       251       
                                                                                                                               103         115
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Y6Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Y6Z)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8IL32_PLAF7 | Q8IL32)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042623    ATPase activity, coupled    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction directly drives some other reaction, for example ion transport across a membrane.
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
biological process
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0009408    response to heat    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    GO:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
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 1y6z)
 
  Sites
(no "Sites" information available for 1y6z)
 
  Cis Peptide Bonds
    Gln B:42 - Ile B:43   [ 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
  1y6z
    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
  Q8IL32_PLAF7 | Q8IL32
    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
  Q8IL32_PLAF7 | Q8IL32
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8IL32_PLAF7 | Q8IL32: 3ied

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1Y6Z)