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(-) Description

Title :  HUMAN PPARDELTA LIGAND-BINDING DOMAIN IN COMPLEXED WITH SPECIFIC AGONIST 1
 
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 :  1.50
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-GOLD(DE3)PLYSS AG'
    Expression System Plasmid: PET28A(+)
    Expression System Taxid: 866768
    Expression System Vector Type: PLASMID
    Gene: PPARD, NR1C2, PPARB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: LIGAND-BINDING DOMAIN
    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  (6, 23)

Asymmetric Unit (6, 23)
No.NameCountTypeFull Name
17UJ2Ligand/Ion6-(2-{[([1,1'-BIPHENYL]-4-CARBONYL)(PROPAN-2-YL)AMINO]METHYL}PHENOXY)HEXANOIC ACID
2B7G2Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3CL2Ligand/IonCHLORIDE ION
4K2Ligand/IonPOTASSIUM ION
5PEG7Ligand/IonDI(HYDROXYETHYL)ETHER
6PGO8Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 1 (4, 10)
No.NameCountTypeFull Name
17UJ1Ligand/Ion6-(2-{[([1,1'-BIPHENYL]-4-CARBONYL)(PROPAN-2-YL)AMINO]METHYL}PHENOXY)HEXANOIC ACID
2B7G1Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3CL-1Ligand/IonCHLORIDE ION
4K-1Ligand/IonPOTASSIUM ION
5PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
6PGO5Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 2 (4, 9)
No.NameCountTypeFull Name
17UJ1Ligand/Ion6-(2-{[([1,1'-BIPHENYL]-4-CARBONYL)(PROPAN-2-YL)AMINO]METHYL}PHENOXY)HEXANOIC ACID
2B7G1Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3CL-1Ligand/IonCHLORIDE ION
4K-1Ligand/IonPOTASSIUM ION
5PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
6PGO3Ligand/IonS-1,2-PROPANEDIOL

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:245 , THR A:252 , THR A:253 , HIS A:287 , LEU A:294 , LEU A:303 , ILE A:328 , LYS A:331 , HIS A:413 , MET A:417 , LEU A:433 , TYR A:437 , HOH A:673 , HOH A:689binding site for residue 7UJ A 501
02AC2SOFTWARELYS A:283 , GLU A:435 , ILE A:436 , HOH A:747 , HOH A:765 , ASN B:276 , VAL B:279 , THR B:280 , B7G B:502binding site for residue B7G A 502
03AC3SOFTWAREARG A:379 , HOH A:696binding site for residue PGO A 503
04AC4SOFTWARETRP A:220 , GLN A:221binding site for residue PEG A 504
05AC5SOFTWARELEU A:219 , TRP A:220 , TYR A:238binding site for residue PEG A 505
06AC6SOFTWARETHR A:252 , THR A:256 , ILE A:290 , MET A:293 , LEU A:294binding site for residue PGO A 506
07AC7SOFTWARELEU A:400binding site for residue PGO A 507
08AC8SOFTWAREGLN A:221 , GLY A:225binding site for residue PGO A 508
09AC9SOFTWAREPRO A:210 , ASN A:299 , PHE A:311binding site for residue PGO A 510
10AD1SOFTWAREASN A:339 , HOH A:656 , HOH A:750binding site for residue K A 511
11AD2SOFTWARETRP B:228 , VAL B:245 , PHE B:246 , CYS B:249 , THR B:252 , THR B:253 , HIS B:287 , LEU B:303 , ILE B:328 , LYS B:331 , HIS B:413 , LEU B:433 , TYR B:437 , PGO B:507 , HOH B:651 , HOH B:664 , HOH B:716binding site for residue 7UJ B 501
12AD3SOFTWAREASN A:276 , VAL A:279 , THR A:280 , B7G A:502 , HOH A:714 , HOH A:749 , LYS B:283 , LEU B:432 , GLU B:435 , LYS B:438 , HOH B:623binding site for residue B7G B 502
13AD4SOFTWARETYR B:394 , PRO B:397 , LYS B:398 , HOH B:607binding site for residue PEG B 503
14AD5SOFTWARELYS B:195 , SER B:199 , LYS B:322 , ASP B:326 , CL B:510 , HOH B:616 , HOH B:731binding site for residue PEG B 504
15AD6SOFTWAREASN B:366 , ARG B:369 , ALA B:372binding site for residue PEG B 505
16AD7SOFTWARETYR B:183 , LYS B:195 , GLU B:412 , GLN B:415 , MET B:416 , CL B:510 , HOH B:601 , HOH B:602 , HOH B:610 , HOH B:629 , HOH B:658binding site for residue PGO B 506
17AD8SOFTWARETHR B:252 , ILE B:290 , LEU B:294 , ILE B:297 , 7UJ B:501 , HOH B:603 , HOH B:640binding site for residue PGO B 507
18AD9SOFTWAREILE B:200 , LEU B:201 , PRO B:210 , ASN B:299binding site for residue PGO B 508
19AE1SOFTWAREASN B:299 , ASN B:339 , HOH B:756binding site for residue CL B 509
20AE2SOFTWARETHR B:193 , PEG B:504 , PGO B:506 , HOH B:786binding site for residue CL B 510
21AE3SOFTWAREASN B:184 , THR B:411 , ALA B:414 , GLN B:415 , GLN B:418 , TYR B:437 , MET B:440 , HOH B:628binding site for residue PEG B 511
22AE4SOFTWAREPRO B:431 , GLU B:435 , HOH B:808 , HOH B:858binding site for residue K B 512

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U3Q)

(-) 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 5U3Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U3Q)

(-) Exons   (0, 0)

(no "Exon" information available for 5U3Q)

(-) 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:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhh....eee.hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee..eeee....eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u3q A 173 ADLKAFSKHIYNAYLKNFNMTKKKARSILTGTAPFVIHDIETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKDMY 441
                                   182       192       202||     216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436     
                                                        203|                                                                                                                                                                                                                                         
                                                         208                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh........eee.hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee..eeee....eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u3q B 170 PQVADLKAFSKHIYNAYLKNFNMTKKKARSILTGKASHTAPFVIHDIETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKDM 440
                                   179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439
   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 5U3Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U3Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U3Q)

(-) Gene Ontology  (81, 81)

Asymmetric Unit(hide GO term definitions)

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  5u3q
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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 5u3r 5u3s 5u3t 5u3u 5u3v 5u3w 5u3x 5u3y 5u3z 5u40 5u41 5u42 5u43 5u44 5u45 5u46

(-) Related Entries Specified in the PDB File

5u3r 5u3s 5u3t 5u3u 5u3v 5u3w 5u3x 5u3y 5u3z 5u40 5u41 5u42 5u44 5u45 5u46