5U3R - JenaLib

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Title :   HUMAN PPARDELTA LIGAND-BINDING DOMAIN IN COMPLEXED WITH SPECIFIC AGONIST 2

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 :   1.95

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

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
	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

		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, 18)

No.	Name	Count	Type	Full Name
1	7V1	2	Ligand/Ion	6-[2-({[4-(FURAN-2-YL)BENZENE-1-CARBONYL](PROPAN-2-YL)AMINO}METHYL)PHENOXY]HEXANOIC ACID
2	B7G	2	Ligand/Ion	HEPTYL-BETA-D-GLUCOPYRANOSIDE
3	PEG	6	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PGO	8	Ligand/Ion	S-1,2-PROPANEDIOL

Biological Unit 1 (4, 11)

No.	Name	Count	Type	Full Name
1	7V1	1	Ligand/Ion	6-[2-({[4-(FURAN-2-YL)BENZENE-1-CARBONYL](PROPAN-2-YL)AMINO}METHYL)PHENOXY]HEXANOIC ACID
2	B7G	2	Ligand/Ion	HEPTYL-BETA-D-GLUCOPYRANOSIDE
3	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PGO	5	Ligand/Ion	S-1,2-PROPANEDIOL

Biological Unit 2 (3, 7)

No.	Name	Count	Type	Full Name
1	7V1	1	Ligand/Ion	6-[2-({[4-(FURAN-2-YL)BENZENE-1-CARBONYL](PROPAN-2-YL)AMINO}METHYL)PHENOXY]HEXANOIC ACID
2	B7G	-1	Ligand/Ion	HEPTYL-BETA-D-GLUCOPYRANOSIDE
3	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PGO	3	Ligand/Ion	S-1,2-PROPANEDIOL

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:274 , LEU A:275 , ASN A:276 , VAL A:279 , THR A:280 , B7G A:503 , HOH A:608 , HOH A:643 , THR B:261 , LYS B:283 , GLU B:435 , ILE B:436 , LYS B:438	binding site for residue B7G A 501
02	AC2	SOFTWARE	TRP A:228 , VAL A:245 , ARG A:248 , CYS A:249 , THR A:252 , THR A:253 , HIS A:287 , LEU A:294 , ILE A:328 , LYS A:331 , HIS A:413 , LEU A:433 , TYR A:437 , PGO A:504 , HOH A:662	binding site for residue 7V1 A 502
03	AC3	SOFTWARE	THR A:261 , LYS A:283 , GLU A:435 , ILE A:436 , LYS A:438 , B7G A:501 , HOH A:682 , HOH A:722 , PHE B:274 , LEU B:275 , ASN B:276 , VAL B:279 , THR B:280 , HOH B:675	binding site for residue B7G A 503
04	AC4	SOFTWARE	THR A:252 , ILE A:290 , MET A:293 , LEU A:294 , 7V1 A:502 , HOH A:605 , HOH A:697 , HOH A:712	binding site for residue PGO A 504
05	AC5	SOFTWARE	LEU A:201 , PRO A:210 , VAL A:212 , ASN A:299 , PHE A:311	binding site for residue PGO A 505
06	AC6	SOFTWARE	LYS A:283 , ILE A:436 , TYR A:437	binding site for residue PGO A 506
07	AC7	SOFTWARE	MET A:365 , ASN A:366 , HOH B:711	binding site for residue PGO A 507
08	AC8	SOFTWARE	LYS A:337 , LYS A:402 , HOH A:619 , HOH A:703 , HOH A:713	binding site for residue PEG A 508
09	AC9	SOFTWARE	ILE A:241 , HOH A:603	binding site for residue PEG A 509
10	AD1	SOFTWARE	THR A:193 , LYS A:195 , LYS A:196 , ARG A:419 , THR A:423 , HOH A:641	binding site for residue PEG A 510
11	AD2	SOFTWARE	SER A:271 , SER A:272 , LEU A:273 , PHE A:274 , LEU A:275 , ARG B:258 , THR B:261 , HOH B:648	binding site for residue PGO A 511
12	AD3	SOFTWARE	VAL B:245 , CYS B:249 , THR B:252 , THR B:253 , HIS B:287 , ILE B:328 , LYS B:331 , HIS B:413 , MET B:417 , LEU B:433 , TYR B:437 , HOH B:677	binding site for residue 7V1 B 501
13	AD4	SOFTWARE	THR B:252 , THR B:256 , MET B:293 , LEU B:294 , HOH B:631	binding site for residue PGO B 502
14	AD5	SOFTWARE	PRO A:431 , MET B:365 , ASN B:366	binding site for residue PGO B 503
15	AD6	SOFTWARE	LEU B:201 , PRO B:210 , ASN B:299 , PHE B:311	binding site for residue PGO B 504
16	AD7	SOFTWARE	LEU B:400 , ARG B:407	binding site for residue PEG B 505
17	AD8	SOFTWARE	VAL B:232 , TYR B:238	binding site for residue PEG B 507

(no "SS Bond" information available for 5U3R)

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 5U3R)

(no "PROSITE Motif" information available for 5U3R)

(no "Exon" information available for 5U3R)

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
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Chain A from PDB  Type:PROTEIN  Length:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh........eee.hhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee..eeee....eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5u3r A 170 PQVADLKAFSKHIYNAYLKNFNMTKKKARSILTGKASHTAPFVIHDIETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 439
                                   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

Chain B from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhhh..eee.hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee..eeeehhh.eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u3r B 173 ADLKAFSKHIYNAYLKNFNMTKKKARSILTGAPFVIHDIETLWQAEKGLVWLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKDM 440
                                   182       192       202||     217       227||     239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439 
                                                        203|                228|                                                                                                                                                                                                                 
                                                         209                 231

Legend:		→ Mismatch	(orange background)
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	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 5U3R)

(no "CATH Domain" information available for 5U3R)

(no "Pfam Domain" information available for 5U3R)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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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, 18)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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SAPs(SNPs)/Variants (0, 0)

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Gene Ontology (81, 81)

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