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(-) Description

Title :  HUMAN PPARDELTA LIGAND-BINDING DOMAIN IN COMPLEXED WITH SPECIFIC AGONIST 15
 
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 :  2.00
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: 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  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
17UD2Ligand/Ion6-[2-({BENZYL[4-(FURAN-3-YL)BENZENE-1-CARBONYL]AMINO}METHYL)PHENOXY]HEXANOIC ACID
2B7G2Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO5Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 1 (4, 7)
No.NameCountTypeFull Name
17UD1Ligand/Ion6-[2-({BENZYL[4-(FURAN-3-YL)BENZENE-1-CARBONYL]AMINO}METHYL)PHENOXY]HEXANOIC ACID
2B7G1Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO2Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 2 (4, 6)
No.NameCountTypeFull Name
17UD1Ligand/Ion6-[2-({BENZYL[4-(FURAN-3-YL)BENZENE-1-CARBONYL]AMINO}METHYL)PHENOXY]HEXANOIC ACID
2B7G1Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PEG1Ligand/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 , LEU A:294 , LEU A:303 , VAL A:305 , VAL A:312 , ILE A:328 , LYS A:331 , HIS A:413 , MET A:417 , LEU A:433 , TYR A:437 , HOH A:619binding site for residue 7UD A 501
02AC2SOFTWAREPRO A:236 , GLN A:250 , CYS A:251 , HIS A:430binding site for residue PEG A 503
03AC3SOFTWAREPRO A:397binding site for residue PGO A 504
04AC4SOFTWAREARG A:198 , THR A:202 , ASN A:299 , HOH A:617binding site for residue PGO A 505
05AC5SOFTWAREVAL A:232 , TYR A:238 , HIS A:244binding site for residue PEG A 506
06AC6SOFTWARETHR A:261 , LEU A:282 , LYS A:283 , GLU A:435 , ILE A:436 , LYS A:438 , HOH A:642 , LEU B:275 , ASN B:276 , VAL B:279 , THR B:280 , B7G B:501binding site for residue B7G A 507
07AC7SOFTWAREASN A:276 , VAL A:279 , THR A:280 , B7G A:507 , HOH A:636 , THR B:261 , LYS B:283 , GLU B:435 , ILE B:436 , LYS B:438binding site for residue B7G B 501
08AC8SOFTWARETRP B:228 , VAL B:245 , ARG B:248 , CYS B:249 , THR B:252 , THR B:253 , HIS B:287 , LEU B:294 , VAL B:305 , VAL B:312 , ILE B:328 , LYS B:331 , HIS B:413 , MET B:417 , TYR B:437 , HOH B:637binding site for residue 7UD B 502
09AC9SOFTWARELEU B:235 , PRO B:236 , CYS B:251 , HIS B:430binding site for residue PEG B 503
10AD1SOFTWARETYR B:284 , ILE B:436 , TYR B:437binding site for residue PGO B 504
11AD2SOFTWARELEU B:400binding site for residue PGO B 505
12AD3SOFTWARETYR B:186 , MET B:192 , THR B:193 , LYS B:194 , MET B:293 , LEU B:294 , SER B:296 , LEU B:348binding site for residue PGO B 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U40)

(-) Cis Peptide Bonds  (3, 4)

Asymmetric Unit
No.Residues
1Lys A:322 -Pro A:323
2Lys B:224 -Gly B:225
3Lys B:322 -Pro B:323

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U40)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U40)

(-) Exons   (0, 0)

(no "Exon" information available for 5U40)

(-) 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..hhhhhhhhhh..eee.hhhhhhhhhhh...hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...ee..eeeehhh.eeeehhhhhh........hhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u40 A 174 DLKAFSKHIYNAYLKNFNMTKKKARSILTAPFVIHDIETLWQAEKGLVWLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYK 438
                                   183       193       209       219       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       
                                                      202|                228|                                                                                                                                                                                                               
                                                       209                 231                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..hhhhhhhhhh........eee.hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...ee..eeee....eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u40 B 174 DLKAFSKHIYNAYLKNFNMTKKKARSILTGKASHTAPFVIHDIETLWQAEKGLVWLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYK 438
                                   183       193       203       213       223    || 239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429         
                                                                                228|                                                                                                                                                                                                           
                                                                                 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 5U40)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U40)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U40)

(-) Gene Ontology  (81, 81)

Asymmetric Unit(hide GO term definitions)

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  5u40
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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 5u41 5u42 5u43 5u44 5u45 5u46

(-) Related Entries Specified in the PDB File

5u3q 5u3r 5u3s 5u3t 5u3u 5u3v 5u3w 5u3x 5u3y 5u3z 5u41 5u42 5u44 5u45 5u46