5U46 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   HUMAN PPARDELTA LIGAND-BINDING DOMAIN IN COMPLEXED WITH GW501516

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, Gw501516, 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

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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	7T1	2	Ligand/Ion	{2-METHYL-4-[({4-METHYL-2-[4-(TRIFLUOROMETHYL)PHENYL]-1,3-THIAZOL-5-YL}METHYL)SULFANYL]PHENOXY}ACETIC ACID
2	B7G	2	Ligand/Ion	HEPTYL-BETA-D-GLUCOPYRANOSIDE
3	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PGO	2	Ligand/Ion	S-1,2-PROPANEDIOL

Biological Unit 1 (4, 6)

No.	Name	Count	Type	Full Name
1	7T1	1	Ligand/Ion	{2-METHYL-4-[({4-METHYL-2-[4-(TRIFLUOROMETHYL)PHENYL]-1,3-THIAZOL-5-YL}METHYL)SULFANYL]PHENOXY}ACETIC ACID
2	B7G	2	Ligand/Ion	HEPTYL-BETA-D-GLUCOPYRANOSIDE
3	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PGO	2	Ligand/Ion	S-1,2-PROPANEDIOL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	7T1	1	Ligand/Ion	{2-METHYL-4-[({4-METHYL-2-[4-(TRIFLUOROMETHYL)PHENYL]-1,3-THIAZOL-5-YL}METHYL)SULFANYL]PHENOXY}ACETIC ACID
2	B7G	-1	Ligand/Ion	HEPTYL-BETA-D-GLUCOPYRANOSIDE
3	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PGO	-1	Ligand/Ion	S-1,2-PROPANEDIOL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:274 , LEU A:275 , ASN A:276 , VAL A:279 , THR A:280 , B7G A:506 , HOH A:611 , HOH A:662 , LYS B:283 , GLU B:435 , ILE B:436 , LYS B:438	binding site for residue B7G A 501
2	AC2	SOFTWARE	GLN A:250 , SER A:428 , LEU A:429 , HIS A:430	binding site for residue PGO A 502
3	AC3	SOFTWARE	ARG A:407	binding site for residue PEG A 503
4	AC4	SOFTWARE	TRP A:228 , PHE A:246 , ARG A:248 , CYS A:249 , THR A:252 , THR A:253 , HIS A:287 , LEU A:294 , VAL A:305 , VAL A:312 , HIS A:413 , MET A:417 , LEU A:433 , TYR A:437	binding site for residue 7T1 A 505
5	AC5	SOFTWARE	THR A:261 , LYS A:283 , GLU A:435 , ILE A:436 , LYS A:438 , B7G A:501 , HOH A:640 , HOH A:675 , LEU B:275 , ASN B:276 , THR B:280	binding site for residue B7G A 506
6	AC6	SOFTWARE	TRP B:228 , VAL B:245 , PHE B:246 , ARG B:248 , CYS B:249 , THR B:253 , HIS B:287 , LEU B:294 , VAL B:312 , HIS B:413 , MET B:417 , LEU B:433 , TYR B:437	binding site for residue 7T1 B 502

(no "SS Bond" information available for 5U46)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 5U46)

(no "PROSITE Motif" information available for 5U46)

(no "Exon" information available for 5U46)

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:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...eee.hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee..eeee....eeeehhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5u46 A 170 PQVADLKAFSKHIYNAYLKNFNMTKKKARSILTAPFVIHDIETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 439
                                   179       189       199  ||   215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435    
                                                          202|                                                                                                                                                                                                                                      
                                                           209

Chain B from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               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........hhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5u46 B 170 PQVADLKAFSKHIYNAYLKNFNMTKKKARSILTAPFVIHDIETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 439
                                   179       189       199  ||   215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435    
                                                          202|                                                                                                                                                                                                                                      
                                                           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 '\|'

(no "SCOP Domain" information available for 5U46)

(no "CATH Domain" information available for 5U46)

(no "Pfam Domain" information available for 5U46)

Asymmetric Unit(hide GO term definitions)

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	Cis Peptide Bonds
		Lys A:322 - Pro A:323	[ RasMol ]
		Lys B:322 - Pro B:323	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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