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(-) Description

Title :  HUMAN PPARDELTA LIGAND-BINDING DOMAIN IN COMPLEXED WITH SPECIFIC AGONIST 8
 
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 :  2.10
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 Plasmid: PET28A(+)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 131-402
    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  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
17U42Ligand/Ion6-[2-({CYCLOPROPYL[4-(PYRIDIN-3-YL)BENZENE-1-CARBONYL]AMINO}METHYL)PHENOXY]HEXANOIC ACID
2B7G2Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO5Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 1 (4, 5)
No.NameCountTypeFull Name
17U41Ligand/Ion6-[2-({CYCLOPROPYL[4-(PYRIDIN-3-YL)BENZENE-1-CARBONYL]AMINO}METHYL)PHENOXY]HEXANOIC ACID
2B7G1Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO2Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
17U41Ligand/Ion6-[2-({CYCLOPROPYL[4-(PYRIDIN-3-YL)BENZENE-1-CARBONYL]AMINO}METHYL)PHENOXY]HEXANOIC ACID
2B7G1Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO3Ligand/IonS-1,2-PROPANEDIOL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:228 , VAL A:245 , ARG A:248 , CYS A:249 , THR A:252 , THR A:253 , HIS A:287 , ILE A:290 , LEU A:294 , VAL A:312 , LYS A:331 , HIS A:413 , MET A:417 , LEU A:433 , TYR A:437 , PGO A:505 , HOH A:620binding site for residue 7U4 A 501
02AC2SOFTWARETHR A:261 , LYS A:283 , GLU A:435 , ILE A:436 , LYS A:438 , PHE B:274 , LEU B:275 , ASN B:276 , VAL B:279 , THR B:280 , B7G B:501 , HOH B:621binding site for residue B7G A 502
03AC3SOFTWARELEU A:201 , VAL A:212 , ASN A:299 , PHE A:311binding site for residue PGO A 503
04AC4SOFTWARETYR A:284 , GLU A:288 , ASP A:360 , ARG A:361 , ARG A:407binding site for residue PEG A 504
05AC5SOFTWARETHR A:252 , THR A:256 , MET A:293 , 7U4 A:501binding site for residue PGO A 505
06AC6SOFTWARELEU A:275 , ASN A:276 , VAL A:279 , THR A:280 , B7G A:502 , HOH A:625 , THR B:261 , LYS B:283 , GLU B:435 , ILE B:436 , LYS B:438binding site for residue B7G B 501
07AC7SOFTWARELEU B:219 , VAL B:245 , ARG B:248 , CYS B:249 , THR B:252 , THR B:253 , HIS B:287 , ILE B:290 , LEU B:294 , VAL B:305 , VAL B:312 , ILE B:328 , LYS B:331 , HIS B:413 , MET B:417 , LEU B:433 , TYR B:437 , HOH B:616binding site for residue 7U4 B 502
08AC8SOFTWARETHR B:411 , HOH B:613binding site for residue PEG B 503
09AC9SOFTWARETHR B:252 , THR B:256 , MET B:293binding site for residue PGO B 504
10AD1SOFTWAREARG B:407binding site for residue PEG B 505
11AD2SOFTWAREASP B:405 , GLN B:408binding site for residue PGO B 506
12AD3SOFTWARELEU B:201 , ASN B:299binding site for residue PGO B 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U3X)

(-) 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 5U3X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U3X)

(-) Exons   (0, 0)

(no "Exon" information available for 5U3X)

(-) 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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhh........eee.hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..eeeehhh.eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u3x A 173 ADLKAFSKHIYNAYLKNFNMTKKKARSILTGKASHTAPFVIHDIETLWQAEKGLVWGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 439
                                   182       192       202       212       222     ||237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437  
                                                                                 228|                                                                                                                                                                                                             
                                                                                  234                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..hhhhhhhhhhh..eee.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..eeee....eeeehhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5u3x B 174 DLKAFSKHIYNAYLKNFNMTKKKARSILTGAPFVIHDIETLWQAEKGLLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYK 438
                                   183       193       203|      218       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436  
                                                       203|              226|                                                                                                                                                                                                           
                                                        209               235
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "SCOP Domain" information available for 5U3X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U3X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U3X)

(-) Gene Ontology  (81, 81)

Asymmetric Unit(hide GO term definitions)

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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 5u3y 5u3z 5u40 5u41 5u42 5u43 5u44 5u45 5u46

(-) Related Entries Specified in the PDB File

5u3q 5u3r 5u3s 5u3t 5u3u 5u3v 5u3w 5u3y 5u3z 5u40 5u41 5u42 5u44 5u45 5u46