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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE AMINO-TERMINAL DOMAIN OF HSP90 FROM LEISHMANIA MAJOR, LMJF33.0312:M1-K213 IN THE PRESENCE OF 17-DMAP-GELDANAMYCIN
 
Authors :  A. K. Wernimont, W. Tempel, Y. H. Lin, A. Hutchinson, F. Mackenzie, A. Fa D. Cossar, Y. Zhao, M. Schapira, C. H. Arrowsmith, A. M. Edwards, C. Bou J. Weigelt, M. A. J. Ferguson, R. Hui, J. C. Pizarro, T. Hills, Structur Genomics Consortium (Sgc)
Date :  28 Dec 10  (Deposition) - 23 Feb 11  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Sleeping Sickness, Leishmania, Heat Shock Protein, Structural Genomics, Structural Genomics Consortium, Sgc, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Wernimont, W. Tempel, Y. H. Lin, A. Hutchinson, F. Mackenzie, A. Fairlamb, D. Cossar, Y. Zhao, M. Schapira, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, M. A. J. Ferguson, R. Hui, J. C. Pizarro, T. Hills
Crystal Structure Of The Amino-Terminal Domain Of Hsp90 Fro Leishmania Major, Lmjf33. 0312:M1-K213 In The Presence Of 17-Dmap-Geldanamycin.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HEAT SHOCK PROTEIN 83-1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LMJF33.0312
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1D1S1Ligand/Ion(4E,6Z,8S,9S,10E,12S,13R,14S,16R)-19-{[3-(DIMETHYLAMINO)PROPYL]AMINO}-13-HYDROXY-8,14-DIMETHOXY-4,10,12,16-TETRAMETHYL-3,20,22-TRIOXO-2-AZABICYCLO[16.3.1]DOCOSA-1(21),4,6,10,18-PENTAEN-9-YLCARBAMATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1D1S2Ligand/Ion(4E,6Z,8S,9S,10E,12S,13R,14S,16R)-19-{[3-(DIMETHYLAMINO)PROPYL]AMINO}-13-HYDROXY-8,14-DIMETHOXY-4,10,12,16-TETRAMETHYL-3,20,22-TRIOXO-2-AZABICYCLO[16.3.1]DOCOSA-1(21),4,6,10,18-PENTAEN-9-YLCARBAMATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:36 , ALA A:37 , ASP A:39 , ALA A:40 , LYS A:43 , ASP A:78 , ILE A:81 , MET A:83 , ASN A:91 , ARG A:97 , GLY A:120 , VAL A:121 , GLY A:122 , PHE A:123 , THR A:169 , ILE A:171 , HOH A:215 , HOH A:216 , HOH A:226 , HOH A:228 , HOH A:238BINDING SITE FOR RESIDUE D1S A 214

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q5J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q5J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q5J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q5J)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q5J)

(-) 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:205
 aligned with Q4Q4I6_LEIMA | Q4Q4I6 from UniProtKB/TrEMBL  Length:701

    Alignment length:215
                                   1                                                                                                                                                                                                               
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203     
         Q4Q4I6_LEIMA     - -------MTETFAFQAEINQLMSLIINTFYSNKEIFLRELISNASDACDKIRYQSLTDPSVLGESPRLCIRVVPDKENKTLTVEDNGIGMTKADLVNNLGTIARSGTKAFMEALEAGGDMSMIGQFGVGFYSAYLVADRVTVTSKNNSDESYVWESSAGGTFTITSTPESDMKRGTRITLHLKEDQMEYLEPRRLKELIKKHSEFIGYDIELMVE 208
               SCOP domains d3q5ja_ A: automated matches                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------HATPase_c_3-3q5jA01 A:23-198                                                                                                                                                    ---------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HSP90-3q5jA02 A:181-208      Pfam domains (2)
         Sec.struct. author ........eeeee.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh-------...eeeeeee....eeeeee.....hhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.eeeeeeeee......eeeee....eeeeee..---...eeeeeeee...hhhhhhhhhhhhhhhhhhhhh..eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q5j A  -6 ENLYFQGMTETFAFQAEINQLMSLIINTFYSNKEIFLRELISNASDACDKIRYQSLTD-------PRLCIRVVPDKENKTLTVEDNGIGMTKADLVNNLGTIARSGTKAFMEALEAGGDMSMIGQFGVGFYSAYLVADRVTVTSKNNSDESYVWESSAGGTFTITSTP---MKRGTRITLHLKEDQMEYLEPRRLKELIKKHSEFIGYDIELMVE 208
                                     3        13        23        33        43       | -     |  63        73        83        93       103       113       123       133       143       153       | - |     173       183       193       203     
                                                                                    51      59                                                                                                   161 165
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q5J)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: His_Kinase_A (147)
(-)
Clan: no clan defined [family: HSP90] (107)
(-)
Family: HSP90 (107)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q4Q4I6_LEIMA | Q4Q4I6)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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: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).

 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
    D1S  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3q5j)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  3q5j
    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
  Q4Q4I6_LEIMA | Q4Q4I6
    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
  Q4Q4I6_LEIMA | Q4Q4I6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q4Q4I6_LEIMA | Q4Q4I6: 3h80 3hjc 3q5k 3q5l 3u67

(-) Related Entries Specified in the PDB File

3h80 3q5i 3q5k 3q5l