5U42 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   HUMAN PPARDELTA LIGAND-BINDING DOMAIN IN COMPLEXED WITH SPECIFIC AGONIST 11

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 :   1.70

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	:	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, 13)

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

Biological Unit 1 (4, 8)

No.	Name	Count	Type	Full Name
1	7SM	1	Ligand/Ion	6-(2-{[CYCLOPROPYL(3'-METHOXY[1,1'-BIPHENYL]-4-CARBONYL)AMINO]METHYL}PHENOXY)HEXANOIC ACID
2	B7G	3	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 2 (3, 5)

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

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:276 , VAL A:279 , THR A:280 , B7G A:508 , HOH A:645 , LYS B:283 , GLU B:435 , ILE B:436 , HOH B:602	binding site for residue B7G A 501
02	AC2	SOFTWARE	LEU A:219 , GLU A:223 , TRP A:228 , VAL 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 , MET A:417 , LEU A:433 , TYR A:437 , PGO A:503 , HOH A:696	binding site for residue 7SM A 502
03	AC3	SOFTWARE	ILE A:290 , LEU A:294 , ILE A:297 , 7SM A:502 , HOH A:603	binding site for residue PGO A 503
04	AC4	SOFTWARE	ARG A:407	binding site for residue PEG A 504
05	AC5	SOFTWARE	ASN A:191 , MET A:192 , THR A:193 , LYS A:195 , LYS A:196 , ARG A:419 , THR A:423 , HOH A:624 , HOH A:659 , HOH A:702	binding site for residue PEG A 505
06	AC6	SOFTWARE	PRO A:210 , VAL A:212	binding site for residue PGO A 506
07	AC7	SOFTWARE	PRO A:236 , CYS A:251 , VAL A:254 , GLU A:255 , ARG A:258 , SER A:428 , HIS A:430 , HOH A:717	binding site for residue B7G A 507
08	AC8	SOFTWARE	THR A:261 , LYS A:283 , LEU A:432 , GLU A:435 , ILE A:436 , LYS A:438 , B7G A:501 , HOH A:688 , LEU B:275 , ASN B:276 , VAL B:279 , THR B:280 , HOH B:681	binding site for residue B7G A 508
09	AC9	SOFTWARE	LEU B:219 , GLU B:223 , TRP B:228 , VAL B:245 , CYS B:249 , THR B:252 , THR B:253 , HIS B:287 , ILE B:290 , LEU B:294 , LEU B:303 , VAL B:305 , ILE B:328 , LYS B:331 , HIS B:413 , MET B:417 , LEU B:433 , TYR B:437 , PGO B:503 , HOH B:666	binding site for residue 7SM B 501
10	AD1	SOFTWARE	ARG B:407	binding site for residue PEG B 502
11	AD2	SOFTWARE	THR B:252 , ILE B:290 , MET B:293 , LEU B:294 , ILE B:297 , 7SM B:501	binding site for residue PGO B 503
12	AD3	SOFTWARE	VAL B:232 , TYR B:238 , HIS B:244	binding site for residue PEG B 504

(no "SS Bond" information available for 5U42)

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 5U42)

(no "PROSITE Motif" information available for 5U42)

(no "Exon" information available for 5U42)

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:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.......eee.hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee..eeee....eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u42 A 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

Chain B from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhh...eee.hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee..eeeehhh.eeeehhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u42 B 173 ADLKAFSKHIYNAYLKNFNMTKKKARSILTGAPFVIHDIETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKDM 440
                                   182       192       202||     217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437   
                                                        203|                                                                                                                                                                                                                                       
                                                         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 5U42)

(no "CATH Domain" information available for 5U42)

(no "Pfam Domain" information available for 5U42)

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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	5u42
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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Gene Ontology (81, 81)

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