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(-) Description

Title :  GRP94 IN COMPLEX WITH THE NOVEL HSP90 INHIBITOR RADESTER AMINE
 
Authors :  R. M. Immormino, D. T. Gewirth
Date :  08 Feb 06  (Deposition) - 06 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Grp94, Hsp82, Hsp90, Htpg, Chaperone, Ligand, Radicicol, Geldanamycin, Radester, Radamide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. M. Immormino, D. T. Gewirth, B. S. Blagg
Inhibittory Ligands Adopt Different Conformations When Bound To Hsp90 Or Grp94: Implications For Paralog-Specific Drug Design
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDOPLASMIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-NB-GRP94
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN, RESIDUES (69-337)
    Gene: TRA1
    Mutation: YES
    Organism Common: DOG
    Organism Scientific: CANIS LUPUS FAMILIARIS
    Organism Taxid: 9615
    Strain: FAMILIARIS
    Synonym: 94 KDA GLUCOSE-REGULATED PROTEIN, GRP94

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2PG48Ligand/IonTETRAETHYLENE GLYCOL
3RDE2Ligand/Ion2-(3-AMINO-2,5,6-TRIMETHOXYPHENYL)ETHYL 5-CHLORO-2,4-DIHYDROXYBENZOATE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:107 , ALA A:111 , ASP A:149 , MET A:154 , PHE A:199 , THR A:245 , ILE A:247 , HOH A:1005 , HOH A:1006BINDING SITE FOR RESIDUE RDE A 1001
02AC2SOFTWAREASN B:107 , ALA B:111 , ASP B:149 , GLY B:153 , MET B:154 , PHE B:199 , THR B:245 , ILE B:247 , HOH B:1007 , HOH B:1009BINDING SITE FOR RESIDUE RDE B 1002
03AC3SOFTWARETHR A:212 , ARG A:237 , THR A:248 , HOH A:1178BINDING SITE FOR RESIDUE PG4 A 501
04AC4SOFTWARELYS A:137 , THR A:148 , TRP A:282 , HOH A:1097 , HOH A:1170BINDING SITE FOR RESIDUE PG4 A 502
05AC5SOFTWAREASP A:110 , LYS A:114 , LEU A:117 , HOH A:1168BINDING SITE FOR RESIDUE PG4 A 503
06AC6SOFTWARETHR B:212 , ARG B:237 , THR B:240 , THR B:248 , HOH B:1024BINDING SITE FOR RESIDUE PG4 B 504
07AC7SOFTWARELYS B:137 , HIS B:146 , THR B:148 , TRP B:282 , HOH B:1003 , HOH B:1125 , HOH B:1151BINDING SITE FOR RESIDUE PG4 B 505
08AC8SOFTWAREASP B:262 , ASN B:266BINDING SITE FOR RESIDUE PG4 B 506
09AC9SOFTWAREASP B:110 , LYS B:114 , LEU B:117BINDING SITE FOR RESIDUE PG4 B 507
10BC1SOFTWAREGLY A:128 , ASN A:129 , ASN A:239 , HOH A:1048BINDING SITE FOR RESIDUE PG4 A 508
11BC2SOFTWAREASN A:83 , LYS A:87 , SER A:227 , HOH A:1060 , ASN B:83 , LYS B:87 , ILE B:90 , SER B:227 , HOH B:1157 , HOH B:1168BINDING SITE FOR RESIDUE 1PE B 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HSP90PS00298 Heat shock hsp90 proteins family signature.ENPL_CANLF94-103
 		  2A:94-103
B:94-103

(-) Exons   (0, 0)

(no "Exon" information available for 2FYP)

(-) 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:232
 aligned with ENPL_CANLF | P41148 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:297
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       
           ENPL_CANLF    41 GSRTDDEVVQREEEAIQLDGLNASQIRELREKSEKFAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKTVWDWELMN 337
               SCOP domains d2                        fypa_ A: HSP90                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2f                        ypA00 A:65-337  [code=3.30.565.10, no name defined]                                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .h------------------------hhhhh...ee..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeee....eeeeee.....hhhhhhhhhhh....hhhhhhhhhhhh......hhhhhhhh.hhhhhhhh.eeeeeeeee......eeeee....eeeee.........eeeeeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeeeee.-----------------------------------------..eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HSP90     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fyp A  65 GS------------------------HMLREKSEKFAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKT-----------------------------------------KTVWDWELMN 337
                             |       -         -      | 70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280     |   -         -         -         -       330       
                             |                       67                                                                                                                                                                                                                        286                                       328         
                            66                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:232
 aligned with ENPL_CANLF | P41148 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:297
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       
           ENPL_CANLF    41 GSRTDDEVVQREEEAIQLDGLNASQIRELREKSEKFAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKTVWDWELMN 337
               SCOP domains d2                        fypb_ B: HSP90                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2f                        ypB00 B:65-337  [code=3.30.565.10, no name defined]                                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .h------------------------hhhhhh..ee..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeee....eeeeee.....hhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.eeeeeeeee......eeeee....eeeee.........eeeeeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeeeee.-----------------------------------------..eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HSP90     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fyp B  65 GS------------------------HMLREKSEKFAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKT-----------------------------------------KTVWDWELMN 337
                             |       -         -      | 70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280     |   -         -         -         -       330       
                            66                       67                                                                                                                                                                                                                        286                                       328
   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  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ENPL_CANLF | P41148)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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).
    GO:0030433    ubiquitin-dependent ERAD pathway    The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    GO:0016529    sarcoplasmic reticulum    A fine reticular network of membrane-limited elements that pervades the sarcoplasm of a muscle cell; continuous over large portions of the cell and with the nuclear envelope; that part of the endoplasmic reticulum specialized for calcium release, uptake and storage.

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  ENPL_CANLF | P41148
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENPL_CANLF | P41148: 1qy5 1qy8 1qye 1tbw 1tc0 1tc6 1u0y 1u0z 1u2o 1ysz 1yt0 1yt1 1yt2 2esa 2exl 2gfd 2gqp 2h8m 2hch 2hg1 2o1t 2o1u 2o1v 2o1w 3o2f 5in9

(-) Related Entries Specified in the PDB File

1bgq RADICICOL BOUND TO THE ATP BINDING SITE OF THE N-TERMINAL DOMAIN OF THE YEAST HSP90 CHAPERONE
1osf HUMAN HSP90 IN COMPLEX WITH 17-DESMETHOXY-17-N, N- DIMETHYLAMINOETHYLAMINO-GELDANAMYCIN
1qy8 CRYSTAL STRUCTURE OF THE N-DOMAIN OF THE ER HSP90 CHAPERONE GRP94 IN COMPLEX WITH RADICICOL
1u0z N-DOMAIN OF GRP94 LACKING THE CHARGED DOMAIN IN COMPLEX WITH RADICICOL
1yet GELDANAMYCIN BOUND TO THE HSP90 GELDANAMYCIN-BINDING DOMAIN
1zwh YEAST HSP82 IN COMPLEX WITH THE NOVEL HSP90 INHIBITOR RADESTER AMINE
2exl GRP94 N-TERMINAL DOMAIN BOUND TO GELDANAMYCIN
2fxs YEAST HSP82 IN COMPLEX WITH THE NOVEL HSP90 INHIBITOR RADAMIDE