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(-) Description

Title :  HUMAN PPAR GAMMA LIGAND BINDING DOMAIN IN COMPLEX WITH A GAMMMA SELECTIVE SYNTHETIC PARTIAL AGONIST MEKT76
 
Authors :  T. Oyama, M. Ohashi, H. Miyachi, M. Kusunoki
Date :  17 Mar 15  (Deposition) - 02 Mar 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nuclear Receptor, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Ohashi, K. Gamo, T. Oyama, H. Miyachi
Peroxisome Proliferator-Activated Receptor Gamma (Ppar Gamm ) Has Multiple Binding Points That Accommodate Ligands In Various Conformations: Structurally Similar Ppar Gamma Partial Agonists Bind To Ppar Gamma Lbd In Different Conformations
Bioorg. Med. Chem. Lett. V. 25 2758 2015
PubMed-ID: 26025876  |  Reference-DOI: 10.1016/J.BMCL.2015.05.025

(-) Compounds

Molecule 1 - PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: LIGAND BINDING DOMAIN, UNP RESIDUES 223-504
    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/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1JJB1Ligand/IonN-(BENZYLSULFONYL)-4-PROPOXY-3-({[4-(PYRIMIDIN-2-YL)BENZOYL]AMINO}METHYL)BENZAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:266 , ILE B:281 , CYS B:285 , ARG B:288 , SER B:289 , ALA B:292 , GLU B:295 , TYR B:327 , MET B:329 , LEU B:330 , LEU B:333 , MET B:364binding site for residue JJB B 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YT1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:358 -Pro A:359
2Lys B:358 -Pro B:359

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YT1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YT1)

(-) Exons   (0, 0)

(no "Exon" information available for 4YT1)

(-) 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:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh........eee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeehhh.eeeehhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yt1 A 205 NPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDL 476
                                   214       224       234       244       254       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475 
                                                                                    263|                                                                                                                                                                                                         
                                                                                     275                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....eee.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh...eeee....eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yt1 B 207 ESADLRALAKHLYDSYIKSFPLTKAKARAILTGKKSPFVIYDMNSLMMGEDKIKFKHKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYK 474
                                   216       226       236   ||  249       259      |277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       
                                                           240|                   266|                                                                                                                                                                                                       
                                                            244                    275
   Legend:   → Mismatch (orange background)
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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 4YT1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YT1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YT1)

(-) Gene Ontology  (107, 107)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4r2u 4r6s 4xld 4xta 4xuh 4xum 4y29 5azv 5dsh 5dv3 5dv6 5dv8 5dvc 5dwl 5f9b 5gtn 5gto 5gtp 5hzc 5ji0 5tto 5two

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4YT1)