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(-) Description

Title :  HUMAN PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA IN COMPLEX WITH ROSIGLITAZONE
 
Authors :  M. V. Liberato, A. S. Nascimento, I. Polikarpov
Date :  11 Apr 12  (Deposition) - 06 Mar 13  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.54
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Nuclear Receptor, Retinoic Acid Receptor, Nucleus, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. V. Liberato, A. S. Nascimento, S. D. Ayers, J. Z. Lin, A. Cvoro, R. L. Silveira, L. Martinez, P. C. Souza, D. Saidemberg, T. Deng, A. A. Amato, M. Togashi, W. A. Hsueh, K. Phillips, M. S. Palma, F. A. Neves, M. S. Skaf, P. Webb, I. Polikarpov
Medium Chain Fatty Acids Are Selective Peroxisome Proliferator Activated Receptor (Ppar) Gamma Activators And Pan-Ppar Partial Agonists
Plos One V. 7 36297 2012
PubMed-ID: 22649490  |  Reference-DOI: 10.1371/JOURNAL.PONE.0036297

(-) Compounds

Molecule 1 - PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: LIGAND BINDING DOMAIN, UNP RESIDUES 235-505
    Gene: PPARG, NR1C3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PPAR-GAMMA, NUCLEAR RECEPTOR SUBFAMILY 1 GROUP C MEMBER 3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1BRL1Ligand/Ion2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL)
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BRL1Ligand/Ion2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL)
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1BRL-1Ligand/Ion2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL)
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1BRL1Ligand/Ion2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:281 , GLY A:284 , CYS A:285 , SER A:289 , HIS A:323 , TYR A:327 , MET A:364 , HIS A:449 , TYR A:473BINDING SITE FOR RESIDUE BRL A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EMA)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys A:358 -Pro A:359
2Lys B:358 -Pro B:359
3Gln B:454 -Val B:455

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EMA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EMA)

(-) Exons   (0, 0)

(no "Exon" information available for 4EMA)

(-) 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:256
                                                                                                                                                                                                                                                                                                
               SCOP domains d4emaa_ A: Peroxisome proliferator activated receptor gamma, PPAR-gamma                                                                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh........eee.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..eeee....eeeehhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ema A 207 ESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY 477
                                   216       226       236       246       256   ||  281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471      
                                                                               260|                                                                                                                                                                                                         
                                                                                276                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains d4emab_ B: Peroxisome proliferator activated receptor gamma, PPAR-gamma                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..hhhhhhhhh......eee.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..eeeehhh.eeeehhhhhh........hhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ema B 207 ESADLRALAKHLYDSYIKSFPLTKAKARAILTGDKSPFVIYDMNSLMMGEDEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVDMSLHPLLQEIYK 474
                                   216       226       236  ||   249       259||     284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454||     470    
                                                          239|              260|                                                                                                                                                                                455|            
                                                           243               276                                                                                                                                                                                 462
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  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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EMA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EMA)

(-) Gene Ontology  (107, 107)

Asymmetric Unit(hide GO term definitions)

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  4ema
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  PPARG_HUMAN | P37231
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 Related Entries

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

UniProtKB/Swiss-Prot
        PPARG_HUMAN | P37231: 1fm6 1fm9 1i7i 1k74 1knu 1nyx 1prg 1rdt 1wm0 1zeo 1zgy 2ath 2f4b 2fvj 2g0g 2g0h 2gtk 2hfp 2hwq 2hwr 2i4j 2i4p 2i4z 2om9 2p4y 2pob 2prg 2q59 2q5p 2q5s 2q61 2q6r 2q6s 2q8s 2qmv 2vsr 2vst 2vv0 2vv1 2vv2 2vv3 2vv4 2xkw 2yfe 2zk0 2zk1 2zk2 2zk3 2zk4 2zk5 2zk6 2zno 2zvt 3ads 3adt 3adu 3adv 3adw 3adx 3an3 3an4 3b0q 3b0r 3b1m 3b3k 3bc5 3cdp 3cds 3cs8 3cwd 3d6d 3dzu 3dzy 3e00 3et0 3et3 3fej 3fur 3g9e 3gbk 3h0a 3ho0 3hod 3ia6 3k8s 3kmg 3lmp 3noa 3osi 3osw 3pba 3po9 3prg 3qt0 3r5n 3r8a 3r8i 3s9s 3sz1 3t03 3ty0 3u9q 3v9t 3v9v 3v9y 3vjh 3vji 3vn2 3vso 3vsp 3wj4 3wj5 3wmh 3x1h 3x1i 4a4v 4a4w 4ci5 4e4k 4e4q 4em9 4f9m 4fgy 4hee 4jaz 4jl4 4l96 4l98 4o8f 4oj4 4prg 4pvu 4pwl 4r06 4r2u 4r6s 4xld 4xta 4xuh 4xum 4y29 4yt1 5azv 5dsh 5dv3 5dv6 5dv8 5dvc 5dwl 5f9b 5gtn 5gto 5gtp 5hzc 5ji0 5tto 5two

(-) Related Entries Specified in the PDB File

1prg LIGAND BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA
1zeo CRYSTAL STRUCTURE OF HUMAN PPAR-GAMMA LIGAND BINDING DOMAIN COMPLEXED WITH AN ALPHA-ARYLOXYPHENYLACETIC ACID AGONIST
2vv1 HPPARGAMMA LIGAND BINDING DOMAIN IN COMPLEX WITH 4-HDHA
3dzu INTACT PPAR GAMMA - RXR ALPHA NUCLEAR RECEPTOR COMPLEX ON DNA BOUND WITH BVT.13, 9-CIS RETINOIC ACID AND NCOA2 PEPTIDE
3dzy INTACT PPAR GAMMA - RXR ALPHA NUCLEAR RECEPTOR COMPLEX ON DNA BOUND WITH ROSIGLITAZONE, 9-CIS RETINOIC ACID AND NCOA2 PEPTIDE
3gwx MOLECULAR RECOGNITION OF FATTY ACIDS BY PEROXISOME PROLIFERATOR-ACTIVATED RECEPTORS
4em9