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(-) Description

Title :  HUMAN PPARDELTA LIGAND-BINDING DOMAIN IN COMPLEXED WITH SPECIFIC AGONIST 13
 
Authors :  C. -C. Wu, T. J. Baiga, M. Downes, J. J. La Clair, A. R. Atkins, S. B. Richa T. A. Stockley-Noel, M. E. Bowman, R. M. Evans, J. P. Noel
Date :  03 Dec 16  (Deposition) - 22 Mar 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ppardelta, Ligand-Binding Domain, Agonist, Protein Binding-Activator Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. C. Wu, T. J. Baiga, M. Downes, J. J. La Clair, A. R. Atkins, S. B. Richard, W. Fan, T. A. Stockley-Noel, M. E. Bowman, J. P. Noel, R. M. Evans
Structural Basis For Specific Ligation Of The Peroxisome Proliferator-Activated Receptor Delta.
Proc. Natl. Acad. Sci. V. 114 E2563 2017 U. S. A.
PubMed-ID: 28320959  |  Reference-DOI: 10.1073/PNAS.1621513114

(-) Compounds

Molecule 1 - PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Fragment: LIGAND-BINDING DOMAIN
    Gene: PPARD, NR1C2, PPARB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PPAR-DELTA,NUCI,NUCLEAR HORMONE RECEPTOR 1,NUC1,NUCLEAR RECEPTOR SUBFAMILY 1 GROUP C MEMBER 2,PEROXISOME PROLIFERATOR- ACTIVATED RECEPTOR BETA,PPAR-BETA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
17SV2Ligand/Ion6-(2-{[CYCLOPROPYL(2'-FLUORO[1,1'-BIPHENYL]-4-CARBONYL)AMINO]METHYL}PHENOXY)HEXANOIC ACID
2B7G2Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PGO3Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
17SV1Ligand/Ion6-(2-{[CYCLOPROPYL(2'-FLUORO[1,1'-BIPHENYL]-4-CARBONYL)AMINO]METHYL}PHENOXY)HEXANOIC ACID
2B7G2Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PGO2Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
17SV1Ligand/Ion6-(2-{[CYCLOPROPYL(2'-FLUORO[1,1'-BIPHENYL]-4-CARBONYL)AMINO]METHYL}PHENOXY)HEXANOIC ACID
2B7G-1Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PGO1Ligand/IonS-1,2-PROPANEDIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:275 , ASN A:276 , VAL A:279 , THR A:280 , B7G A:505 , HOH A:618 , THR B:261 , LYS B:283 , GLU B:435 , ILE B:436 , LYS B:438binding site for residue B7G A 501
2AC2SOFTWARETYR A:186 , MET A:192 , MET A:293 , SER A:296 , PGO A:503binding site for residue PGO A 502
3AC3SOFTWARETHR A:252 , THR A:256 , PGO A:502binding site for residue PGO A 503
4AC4SOFTWARELEU A:219 , VAL A:245 , PHE A:246 , CYS A:249 , THR A:252 , THR A:253 , HIS A:287 , ILE A:290 , LEU A:294 , LEU A:303 , VAL A:305 , LEU A:317 , ILE A:328 , LYS A:331 , HIS A:413 , MET A:417 , TYR A:437 , HOH A:624binding site for residue 7SV A 504
5AC5SOFTWARETHR A:261 , VAL A:279 , LYS A:283 , GLU A:435 , LYS A:438 , B7G A:501 , HOH A:616 , ASN B:276 , THR B:280binding site for residue B7G A 505
6AC6SOFTWARETHR B:252 , ILE B:290binding site for residue PGO B 501
7AC7SOFTWARELEU B:219 , VAL B:245 , PHE B:246 , CYS B:249 , THR B:252 , THR B:253 , HIS B:287 , ILE B:290 , LEU B:294 , LEU B:303 , VAL B:305 , LEU B:317 , ILE B:328 , LYS B:331 , HIS B:413 , MET B:417 , LEU B:433 , TYR B:437 , HOH B:612binding site for residue 7SV B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U44)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:322 -Pro A:323
2Lys B:322 -Pro B:323

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U44)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U44)

(-) Exons   (0, 0)

(no "Exon" information available for 5U44)

(-) 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:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..hhhhhhhhhhh.......eee.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee..eeee....eeeehhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u44 A 174 DLKAFSKHIYNAYLKNFNMTKKKARSILTGKASHTAPFVIHDIETLWQAEKGGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYK 438
                                   183       193       203       213       223 ||    241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       
                                                                             225|                                                                                                                                                                                                            
                                                                              234                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh..hhhhhhhhhh........eee.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee..eeee....eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u44 B 172 VADLKAFSKHIYNAYLKNFNMTKKKARSILTGKASHTAPFVIHDIETLWQAEKGLGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYK 438
                                   181       191       201       211       221    || 238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438
                                                                                226|                                                                                                                                                                                                            
                                                                                 234
   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 5U44)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U44)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U44)

(-) Gene Ontology  (81, 81)

Asymmetric Unit(hide GO term definitions)

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  5u44
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  PPARD_HUMAN | Q03181
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 Related Entries

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

UniProtKB/Swiss-Prot
        PPARD_HUMAN | Q03181: 1gwx 1y0s 2awh 2b50 2baw 2env 2gwx 2j14 2q5g 2xyj 2xyw 2xyx 2znp 2znq 3d5f 3dy6 3et2 3gwx 3gz9 3oz0 3peq 3sp9 3tkm 5u3q 5u3r 5u3s 5u3t 5u3u 5u3v 5u3w 5u3x 5u3y 5u3z 5u40 5u41 5u42 5u43 5u45 5u46

(-) Related Entries Specified in the PDB File

5u3q 5u3r 5u3s 5u3t 5u3u 5u3v 5u3w 5u3x 5u3y 5u3z 5u40 5u41 5u42 5u43 5u45 5u46