5U41 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   HUMAN PPARDELTA LIGAND-BINDING DOMAIN IN COMPLEXED WITH SPECIFIC AGONIST 16

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 :   1.90

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
	Fragment	:	UNP RESIDUES 131-402
	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 (5, 14)

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

Biological Unit 1 (3, 8)

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

Biological Unit 2 (3, 5)

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

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP A:228 , VAL A:245 , CYS A:249 , THR A:252 , THR A:253 , HIS A:287 , LEU A:294 , VAL A:298 , VAL A:305 , ILE A:328 , LYS A:331 , HIS A:413 , TYR A:437 , HOH A:636	binding site for residue 7UG A 501
02	AC2	SOFTWARE	GLN A:230 , CYS A:251 , GLU A:255 , ARG A:258 , HIS A:430 , PGO A:507 , HOH A:612	binding site for residue PEG A 502
03	AC3	SOFTWARE	ARG A:407 , HOH A:601	binding site for residue PEG A 503
04	AC4	SOFTWARE	THR A:252 , HOH A:606 , HOH A:636	binding site for residue PGO A 504
05	AC5	SOFTWARE	THR A:427 , SER A:428 , LEU A:429 , GLN A:434	binding site for residue PGO A 505
06	AC6	SOFTWARE	VAL A:232 , HIS A:244 , HOH A:620	binding site for residue PGO A 506
07	AC7	SOFTWARE	PRO A:236 , TYR A:247 , GLN A:250 , SER A:428 , HIS A:430 , PEG A:502	binding site for residue PGO A 507
08	AC8	SOFTWARE	PHE A:396 , LEU A:400 , HOH A:605	binding site for residue PEG A 508
09	AC9	SOFTWARE	PHE A:274 , ASN A:276 , VAL A:279 , THR A:280 , THR B:261 , LYS B:283 , GLU B:435 , ILE B:436 , LYS B:438 , B7G B:502 , HOH B:609	binding site for residue B7G B 501
10	AD1	SOFTWARE	LYS A:283 , GLU A:435 , ILE A:436 , LYS A:438 , HOH A:627 , LEU B:275 , ASN B:276 , VAL B:279 , THR B:280 , B7G B:501 , HOH B:653	binding site for residue B7G B 502
11	AD2	SOFTWARE	LEU B:219 , VAL B:245 , ARG B:248 , CYS B:249 , THR B:252 , THR B:253 , HIS B:287 , LEU B:294 , VAL B:298 , VAL B:305 , VAL B:312 , ILE B:328 , LYS B:331 , HIS B:413 , LEU B:433 , TYR B:437 , HOH B:630	binding site for residue 7UG B 503
12	AD3	SOFTWARE	ARG B:407	binding site for residue PEG B 504
13	AD4	SOFTWARE	LEU B:235 , PRO B:236 , CYS B:251 , GLU B:255 , HIS B:430 , HOH B:602 , HOH B:610 , HOH B:620	binding site for residue PEG B 505
14	AD5	SOFTWARE	ARG B:198 , VAL B:298 , ASN B:339 , HOH B:670	binding site for residue K B 506

(no "SS Bond" information available for 5U41)

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 5U41)

(no "PROSITE Motif" information available for 5U41)

(no "Exon" information available for 5U41)

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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..hhhhhhhhhh..eee.hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...ee..eeeehhh.eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u41 A 174 DLKAFSKHIYNAYLKNFNMTKKKARSILTAPFVIHDIETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 439
                                   183       193       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439
                                                      202|                                                                                                                                                                                                                                      
                                                       209

Chain B from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhh..eee.hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...ee..eeeehhh.eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u41 B 173 ADLKAFSKHIYNAYLKNFNMTKKKARSILTAPFVIHDIETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 439
                                   182       192       202|      218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438 
                                                       202|                                                                                                                                                                                                                                      
                                                        209

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 5U41)

(no "CATH Domain" information available for 5U41)

(no "Pfam Domain" information available for 5U41)

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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	5u41
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (81, 81)

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