Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF A HSP90 INHIBITOR BOUND TO THE N-TERMINUS OF YEAST HSP90.
 
Authors :  S. M. Roe, L. H. Pearl, C. Prodromou
Date :  04 May 05  (Deposition) - 29 Sep 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Chaperone/Complex, 3D-Structure, Atp-Binding, Chaperone, Heat Shock, Inhibitor, Multigene Family (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. -M. J. Cheung, T. P. Matthews, K. James, M. G. Rowlands, K. J. Boxall, S. Y. Sharp, A. Maloney, S. M. Roe, C. Prodromou, L. H. Pearl, G. W. Aherne, E. Mcdonald, P. Workman
The Identification, Synthesis, Protein Crystal Structure And In Vitro Biochemical Evaluation Of A New 3, 4-Diarylpyrazole Class Of Hsp90 Inhibitors.
Bioorg. Med. Chem. Lett. V. 15 3338 2005
PubMed-ID: 15955698  |  Reference-DOI: 10.1016/J.BMCL.2005.05.046

(-) Compounds

Molecule 1 - ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentN-TERMINUS, RESIDUES 1-219
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymHSP90,HEAT SHOCK PROTEIN HSP90,82 KDA HEAT SHOCK PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1KJ22Ligand/Ion4-{4-[4-(3-AMINOPROPOXY)PHENYL]-1H-PYRAZOL-5-YL}-6-CHLOROBENZENE-1,3-DIOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1KJ21Ligand/Ion4-{4-[4-(3-AMINOPROPOXY)PHENYL]-1H-PYRAZOL-5-YL}-6-CHLOROBENZENE-1,3-DIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1KJ21Ligand/Ion4-{4-[4-(3-AMINOPROPOXY)PHENYL]-1H-PYRAZOL-5-YL}-6-CHLOROBENZENE-1,3-DIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:37 , ASP A:40 , ALA A:41 , ASP A:79 , ILE A:82 , GLY A:83 , MET A:84 , GLY A:121 , PHE A:124 , THR A:171 , LEU A:173 , HOH A:2101 , HOH A:2120BINDING SITE FOR RESIDUE KJ2 A1214
2AC2SOFTWAREASN B:37 , ASP B:40 , ALA B:41 , ASP B:79 , ILE B:82 , GLY B:83 , MET B:84 , GLY B:121 , PHE B:124 , THR B:171 , LEU B:173 , HOH B:2057 , HOH B:2134BINDING SITE FOR RESIDUE KJ2 B1220

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BRE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HSP90PS00298 Heat shock hsp90 proteins family signature.HSP82_YEAST24-33
 
  2A:24-33
B:24-33
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HSP90PS00298 Heat shock hsp90 proteins family signature.HSP82_YEAST24-33
 
  1A:24-33
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HSP90PS00298 Heat shock hsp90 proteins family signature.HSP82_YEAST24-33
 
  1-
B:24-33

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPL240C1YPL240C.1XVI:98625-964962130HSP82_YEAST1-7097092A:2-214
B:2-219
213
218

(-) Sequences/Alignments

Asymmetric 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:213
 aligned with HSP82_YEAST | P02829 from UniProtKB/Swiss-Prot  Length:709

    Alignment length:213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
          HSP82_YEAST     2 ASETFEFQAEITQLMSLIINTVYSNKEIFLRELISNASDALDKIRYKSLSDPKQLETEPDLFIRITPKPEQKVLEIRDSGIGMTKAELINNLGTIAKSGTKAFMEALSAGADVSMIGQFGVGFYSLFLVADRVQVISKSNDDEQYIWESNAGGSFTVTLDEVNERIGRGTILRLFLKDDQLEYLEEKRIKEVIKRHSEFVAYPIQLVVTKEVE 214
               SCOP domains d2brea_ A: HSP90                                                                                                                                                                                                      SCOP domains
               CATH domains 2breA00 A:2-214  [code=3.30.565.10, no name defined]                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeeehhh.eeeeee.....hhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.eeeeeeeee......eeeee....eeeeee.........eeeeeeee...hhhhhhhhhhhhhhhhhh......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------HSP90     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-214 UniProt: 1-709 [INCOMPLETE]                                                                                                                                                                    Transcript 1
                 2bre A   2 ASETFEFQAEITQLMSLIINTVYSNKEIFLRELISNASDALDKIRYKSLSDPKQLETEPDLFIRITPKPEQKVLEIRDSGIGMTKAELINNLGTIAKSGTKAFMEALSAGADVSMIGQFGVGFYSLFLVADRVQVISKSNDDEQYIWESNAGGSFTVTLDEVNERIGRGTILRLFLKDDQLEYLEEKRIKEVIKRHSEFVAYPIQLVVTKEVE 214
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   

Chain B from PDB  Type:PROTEIN  Length:218
 aligned with HSP82_YEAST | P02829 from UniProtKB/Swiss-Prot  Length:709

    Alignment length:218
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        
          HSP82_YEAST     2 ASETFEFQAEITQLMSLIINTVYSNKEIFLRELISNASDALDKIRYKSLSDPKQLETEPDLFIRITPKPEQKVLEIRDSGIGMTKAELINNLGTIAKSGTKAFMEALSAGADVSMIGQFGVGFYSLFLVADRVQVISKSNDDEQYIWESNAGGSFTVTLDEVNERIGRGTILRLFLKDDQLEYLEEKRIKEVIKRHSEFVAYPIQLVVTKEVEKEVPI 219
               SCOP domains d2breb_ B: HSP90                                                                                                                                                                                                           SCOP domains
               CATH domains 2breB00 B:2-219  [code=3.30.565.10, no name defined]                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeeehhh.eeeeee.....hhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.eeeeeeeee......eeeee....eeeeee.........eeeeeeee...hhhhhhhhhhhhhhhhhh......eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------HSP90     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:2-219 UniProt: 1-709 [INCOMPLETE]                                                                                                                                                                         Transcript 1
                 2bre B   2 ASETFEFQAEITQLMSLIINTVYSNKEIFLRELISNASDALDKIRYKSLSDPKQLETEPDLFIRITPKPEQKVLEIRDSGIGMTKAELINNLGTIAKSGTKAFMEALSAGADVSMIGQFGVGFYSLFLVADRVQVISKSNDDEQYIWESNAGGSFTVTLDEVNERIGRGTILRLFLKDDQLEYLEEKRIKEVIKRHSEFVAYPIQLVVTKEVEKEVPI 219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        

   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 Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BRE)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HSP82_YEAST | P02829)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
biological process
    GO:0006458    'de novo' protein folding    The process of assisting in the folding of a nascent peptide chain into its correct tertiary structure.
    GO:0000492    box C/D snoRNP assembly    The aggregation, arrangement and bonding together of proteins and a box C/D snoRNA to form a box C/D small nucleolar ribonucleoprotein (snoRNP) complex.
    GO:0032212    positive regulation of telomere maintenance via telomerase    Any process that activates or increases the frequency, rate or extent of the addition of telomeric repeats by telomerase.
    GO:0043248    proteasome assembly    The aggregation, arrangement and bonding together of a mature, active proteasome complex.
    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:0042026    protein refolding    The process carried out by a cell that restores the biological activity of an unfolded or misfolded protein, using helper proteins such as chaperones.
    GO:0006626    protein targeting to mitochondrion    The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
    GO:0032204    regulation of telomere maintenance    Any process that modulates the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA.
    GO:0006970    response to osmotic 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 stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric 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
    KJ2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2bre)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) 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
  2bre
    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
  HSP82_YEAST | P02829
    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
  HSP82_YEAST | P02829
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        HSP82_YEAST | P028291a4h 1ah6 1ah8 1am1 1amw 1bgq 1hk7 1us7 1usu 1usv 1zw9 1zwh 2akp 2brc 2cg9 2cge 2cgf 2fxs 2iws 2iwu 2iwx 2lsv 2vw5 2vwc 2wep 2weq 2wer 2xd6 2xx2 2xx4 2xx5 2yga 2yge 2ygf 3c0e 3c11 3fp2 4as9 4asa 4asb 4asf 4asg 4ce1 4ce2 4ce3 5mgx

(-) Related Entries Specified in the PDB File

1a4h STRUCTURE OF THE N-TERMINAL DOMAIN OF THE YEAST HSP90 CHAPERONE IN COMPLEX WITH GELDANAMYCIN
1ah6 STRUCTURE OF THE TETRAGONAL FORM OF THE N -TERMINAL DOMAIN OF THE YEAST HSP90 CHAPERONE
1ah8 STRUCTURE OF THE ORTHORHOMBIC FORM OF THE N-TERMINAL DOMAIN OF THE YEAST HSP90 CHAPERONE
1am1 ATP BINDING SITE IN THE HSP90 MOLECULAR CHAPERONE
1amw ADP BINDING SITE IN THE HSP90 MOLECULAR CHAPERONE
1bgq RADICICOL BOUND TO THE ATP BINDING SITE OF THE N-TERMINAL DOMAIN OF THE YEAST HSP90 CHAPERONE
1hk7 MIDDLE DOMAIN OF HSP90
1us7 COMPLEX OF HSP90 AND P50
1usu THE STRUCTURE OF THE COMPLEX BETWEEN AHA1 AND HSP90
1usv THE STRUCTURE OF THE COMPLEX BETWEEN AHA1 AND HSP90
2brc THE STRUCTURE OF THE COMPLEX BETWEEN CT5 AND HSP90