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(-) Description

Title :  CRYSTAL STRUCTURE OF PPARGAMMA IN COMPLEX WITH SR1664
 
Authors :  D. P. Marciano, T. Kamenecka, P. R. Griffin, J. B. Bruning
Date :  13 Aug 14  (Deposition) - 01 Jul 15  (Release) - 01 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  A (1x),D (1x)
Keywords :  Nuclear Receptor Ligand Binding Domain, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. P. Marciano, D. S. Kuruvilla, S. V. Boregowda, A. Asteian, T. S. Hughes, R. Garcia-Ordonez, C. A. Corzo, T. M. Khan, S. J. Novick, H. Park, D. J. Kojetin, D. G. Phinney, J. B. Bruning, T. M. Kamenecka, P. R. Griffin
Pharmacological Repression Of Ppar Gamma Promotes Osteogenesis.
Nat Commun V. 6 7443 2015
PubMed-ID: 26068133  |  Reference-DOI: 10.1038/NCOMMS8443

(-) Compounds

Molecule 1 - PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 231-505
    Gene: NR1C3, PPARG
    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 : AD
Biological Unit 1 (1x): AD
Biological Unit 2 (1x): A (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
13JX2Ligand/Ion4'-[(2,3-DIMETHYL-5-{[(1S)-1-(4-NITROPHENYL)ETHYL]CARBAMOYL}-1H-INDOL-1-YL)METHYL]BIPHENYL-2-CARBOXYLIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
13JX2Ligand/Ion4'-[(2,3-DIMETHYL-5-{[(1S)-1-(4-NITROPHENYL)ETHYL]CARBAMOYL}-1H-INDOL-1-YL)METHYL]BIPHENYL-2-CARBOXYLIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
13JX1Ligand/Ion4'-[(2,3-DIMETHYL-5-{[(1S)-1-(4-NITROPHENYL)ETHYL]CARBAMOYL}-1H-INDOL-1-YL)METHYL]BIPHENYL-2-CARBOXYLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:282 , GLY A:284 , CYS A:285 , GLN A:286 , ARG A:288 , SER A:289 , HIS A:323 , TYR A:327 , LEU A:330 , ILE A:341 , SER A:342 , PHE A:363 , MET A:364 , LYS A:367 , HIS A:449 , LEU A:453 , LEU A:465 , TYR A:473 , HOH A:671BINDING SITE FOR RESIDUE 3JX A 501
2AC2SOFTWAREHIS D:266 , ILE D:281 , PHE D:282 , GLN D:286 , ARG D:288 , SER D:289 , ILE D:326 , TYR D:327 , LEU D:330 , ILE D:341 , SER D:342 , MET D:364 , LYS D:367 , HIS D:449 , LEU D:453BINDING SITE FOR RESIDUE 3JX D 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R2U)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Lys A:261 -Ile A:262
2Lys A:358 -Pro A:359
3Ser D:208 -Ala D:209
4Thr D:242 -Asp D:243
5Lys D:358 -Pro D:359

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R2U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R2U)

(-) Exons   (0, 0)

(no "Exon" information available for 4R2U)

(-) 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......eee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..eeee....eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r2u A 205 NPESADLRALAKHLYDSYIKSFPLTKAKARAILTGTDKSPFVIYDMNSLMMGEDKIKSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDL 476
                                   214       224       234    || 246       256      |276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476
                                                            239|                  263|                                                                                                                                                                                                          
                                                             242                   274                                                                                                                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh..hhhhhhhhhhh.......eee.hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.ee..eeeehhh.eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r2u D 208 SADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTEHPLLQEIYKD 475
                                   217       227       237       247       257       267||     283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453      |468       
                                                                                      268|                                                                                                                                                                                      460|         
                                                                                       275                                                                                                                                                                                       466
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 4R2U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R2U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R2U)

(-) Gene Ontology  (107, 107)

Asymmetric Unit(hide GO term definitions)

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    Lys A:261 - Ile A:262   [ RasMol ]  
    Lys A:358 - Pro A:359   [ RasMol ]  
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    Thr D:242 - Asp D:243   [ RasMol ]  
 
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  4r2u
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  PPARG_HUMAN | P37231
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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 4ema 4f9m 4fgy 4hee 4jaz 4jl4 4l96 4l98 4o8f 4oj4 4prg 4pvu 4pwl 4r06 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

4r6s