Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  HUMAN PPARDELTA LIGAND-BINDING DOMAIN IN COMPLEXED WITH SPECIFIC AGONIST 10
 
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 :  1.72
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  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
17UA2Ligand/Ion6-[2-({CYCLOPROPYL[4-(FURAN-3-YL)BENZENE-1-CARBONYL]AMINO}METHYL)PHENOXY]HEXANOIC ACID
2B7G3Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PEG5Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO5Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 1 (4, 9)
No.NameCountTypeFull Name
17UA1Ligand/Ion6-[2-({CYCLOPROPYL[4-(FURAN-3-YL)BENZENE-1-CARBONYL]AMINO}METHYL)PHENOXY]HEXANOIC ACID
2B7G2Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO4Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 2 (4, 6)
No.NameCountTypeFull Name
17UA1Ligand/Ion6-[2-({CYCLOPROPYL[4-(FURAN-3-YL)BENZENE-1-CARBONYL]AMINO}METHYL)PHENOXY]HEXANOIC ACID
2B7G1Ligand/IonHEPTYL-BETA-D-GLUCOPYRANOSIDE
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
4PGO1Ligand/IonS-1,2-PROPANEDIOL

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:245 , ARG A:248 , CYS A:249 , THR A:252 , THR A:253 , HIS A:287 , ILE A:290 , LEU A:294 , LEU A:303 , ILE A:328 , LYS A:331 , HIS A:413 , LEU A:433 , TYR A:437 , HOH A:644binding site for residue 7UA A 501
02AC2SOFTWARETYR A:284 , ILE A:436 , TYR A:437 , HOH A:675binding site for residue PGO A 502
03AC3SOFTWAREHOH A:612binding site for residue PEG A 503
04AC4SOFTWARETHR A:252 , THR A:256 , ILE A:290 , LEU A:294binding site for residue PGO A 504
05AC5SOFTWAREGLN A:230 , PRO A:236 , TYR A:247 , CYS A:251 , GLU A:255 , ARG A:258 , SER A:428 , HIS A:430 , PEG A:506binding site for residue B7G A 505
06AC6SOFTWARETHR A:427 , SER A:428 , LEU A:429 , GLN A:434 , B7G A:505binding site for residue PEG A 506
07AC7SOFTWARELEU A:201 , PRO A:210 , ASN A:299binding site for residue PGO A 507
08AC8SOFTWARETHR A:261 , LYS A:283 , GLU A:435 , ILE A:436 , LYS A:438 , HOH A:658 , ASN B:276 , THR B:280 , B7G B:501 , HOH B:658binding site for residue B7G A 508
09AC9SOFTWARESER A:271 , SER A:272 , LEU A:273 , PHE A:274 , LEU A:275 , GLN A:278 , THR B:261 , GLU B:262 , LYS B:265 , B7G B:501 , HOH B:616binding site for residue PGO A 509
10AD1SOFTWARELEU A:275 , ASN A:276 , VAL A:279 , THR A:280 , B7G A:508 , PGO A:509 , HOH A:638 , LYS B:283 , GLU B:435 , ILE B:436 , LYS B:438 , HOH B:619binding site for residue B7G B 501
11AD2SOFTWAREVAL B:245 , PHE B:246 , ARG B:248 , CYS B:249 , THR B:252 , THR B:253 , HIS B:287 , ILE B:290 , LEU B:294 , VAL B:305 , ILE B:328 , LYS B:331 , HIS B:413 , MET B:417 , LEU B:433 , TYR B:437 , HOH B:651binding site for residue 7UA B 502
12AD3SOFTWARETRP B:220 , GLN B:221binding site for residue PEG B 503
13AD4SOFTWAREARG B:407binding site for residue PEG B 504
14AD5SOFTWARELYS B:283 , TYR B:284 , HIS B:287 , VAL B:410 , ILE B:436binding site for residue PGO B 505
15AD6SOFTWAREARG A:258 , THR A:261 , SER B:271 , SER B:272 , LEU B:273 , PHE B:274 , LEU B:275binding site for residue PEG B 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U3Z)

(-) 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 5U3Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U3Z)

(-) Exons   (0, 0)

(no "Exon" information available for 5U3Z)

(-) 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:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh........eee.hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee..eeeehhh.eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u3z A 172 VADLKAFSKHIYNAYLKNFNMTKKKARSILTGKASHTAPFVIHDIETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 439
                                   181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431        


Chain B from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..hhhhhhhhhhh..eee.hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee..eeeehhh.eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u3z B 174 DLKAFSKHIYNAYLKNFNMTKKKARSILTGAPFVIHDIETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 439
                                   183       193       203|      218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438 
                                                       203|                                                                                                                                                                                                                                      
                                                        209
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 5U3Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U3Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U3Z)

(-) Gene Ontology  (81, 81)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    7UA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    B7G  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PGO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:322 - Pro A:323   [ RasMol ]  
    Lys B:322 - Pro B:323   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5u3z
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PPARD_HUMAN | Q03181
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PPARD_HUMAN | Q03181
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 5u40 5u41 5u42 5u43 5u44 5u45 5u46

(-) Related Entries Specified in the PDB File

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