BMRB Entry 17977

Name: PPARgamma LBD complexed with MRL20
Published: 2012-01-18

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17977

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

PPARgamma LBD complexed with MRL20

Deposition date:

2011-10-05

Original release date:

2012-01-18

Authors:

Kojetin, Douglas

Citation:

Citation: Hughes, Travis; Chalmers, Michael; Novick, Scott; Kuruvilla, Dana; Chang, Mi Ra; Kamenecka, Theodore; Rance, Mark; Johnson, Bruce; Burris, Thomas; Griffin, Patrick; Kojetin, Douglas. "Ligand and Receptor Dynamics Contribute to the Mechanism of Graded PPAR Agonism." Structure 20, 139-150 (2012).
PubMed: 22244763

Assembly members:

Assembly members:
PPARgamma_LBD, polymer, 276 residues, Formula weight is not available
240, non-polymer, 527.488 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-46

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PPARgamma_LBD: GQLNPESADLRALAKHLYDS YIKSFPLTKAKARAILTGKT TDKSPFVIYDMNSLMMGEDK IKFKHITPLQEQSKEVAIRI FQGCQFRSVEAVQEITEYAK SIPGFVNLDLNDQVTLLKYG VHEIIYTMLASLMNKDGVLI SEGQGFMTREFLKSLRKPFG DFMEPKFEFAVKFNALELDD SDLAIFIAVIILSGDRPGLL NVKPIEDIQDNLLQALELQL KLNHPESSQLFAKLLQKMTD LRQIVTEHVQLLQVIKKTET DMSLHPLLQEIYKDLY

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	499
15N chemical shifts	169
1H chemical shifts	170

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PPARgamma_LBD	1
2	MRL20	2

Entities:

Entity 1, PPARgamma_LBD 276 residues - Formula weight is not available

1

GLY

GLN

LEU

ASN

PRO

GLU

SER

ALA

ASP

LEU

2

ARG

ALA

LEU

ALA

LYS

HIS

LEU

TYR

ASP

SER

3

TYR

ILE

LYS

SER

PHE

PRO

LEU

THR

LYS

ALA

4

LYS

ALA

ARG

ALA

ILE

LEU

THR

GLY

LYS

THR

5

THR

ASP

LYS

SER

PRO

PHE

VAL

ILE

TYR

ASP

6

MET

ASN

SER

LEU

MET

GLY

GLU

ASP

LYS

7

ILE

LYS

PHE

LYS

HIS

ILE

THR

PRO

LEU

GLN

8

GLU

GLN

SER

LYS

GLU

VAL

ALA

ILE

ARG

ILE

9

PHE

GLN

GLY

CYS

GLN

PHE

ARG

SER

VAL

GLU

10

ALA

VAL

GLN

GLU

ILE

THR

GLU

TYR

ALA

LYS

11

SER

ILE

PRO

GLY

PHE

VAL

ASN

LEU

ASP

LEU

12

ASN

ASP

GLN

VAL

THR

LEU

LYS

TYR

GLY

13

VAL

HIS

GLU

ILE

TYR

THR

MET

LEU

ALA

14

SER

LEU

MET

ASN

LYS

ASP

GLY

VAL

LEU

ILE

15

SER

GLU

GLY

GLN

GLY

PHE

MET

THR

ARG

GLU

16

PHE

LEU

LYS

SER

LEU

ARG

LYS

PRO

PHE

GLY

17

ASP

PHE

MET

GLU

PRO

LYS

PHE

GLU

PHE

ALA

18

VAL

LYS

PHE

ASN

ALA

LEU

GLU

LEU

ASP

19

SER

ASP

LEU

ALA

ILE

PHE

ILE

ALA

VAL

ILE

20

ILE

LEU

SER

GLY

ASP

ARG

PRO

GLY

LEU

21

ASN

VAL

LYS

PRO

ILE

GLU

ASP

ILE

GLN

ASP

22

ASN

LEU

GLN

ALA

LEU

GLU

LEU

GLN

LEU

23

LYS

LEU

ASN

HIS

PRO

GLU

SER

GLN

LEU

24

PHE

ALA

LYS

LEU

GLN

LYS

MET

THR

ASP

25

LEU

ARG

GLN

ILE

VAL

THR

GLU

HIS

VAL

GLN

26

LEU

GLN

VAL

ILE

LYS

THR

GLU

THR

27

ASP

MET

SER

LEU

HIS

PRO

LEU

GLN

GLU

28

ILE

TYR

LYS

ASP

LEU

TYR

Entity 2, MRL20 - C28 H24 F3 N O6 - 527.488 Da.

1

240

Samples:

sample_1: PPARgamma LBD, [U-100% 13C; U-100% 15N; U-80% 2H], 1 mM; MRL20 1 mM

sample_conditions_1: ionic strength: 50 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D TROSY-HNCO	sample_1	isotropic	sample_conditions_1
3D TROSY-HNCA	sample_1	isotropic	sample_conditions_1
3D TROSY-HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D TROSY-HN(CA)CB	sample_1	isotropic	sample_conditions_1
3D TROSY-HN(COCA)CB	sample_1	isotropic	sample_conditions_1
3D 1H-15N TROSY-NOESY-HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_1	isotropic	sample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - chemical shift assignment, data analysis

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

Bruker Avance 700 MHz

Related Database Links:

BMRB	15518 17975 17976
PDB	1FM6 1FM9 1I7I 1K74 1KNU 1NYX 1PRG 1RDT 1WM0 1ZEO 1ZGY 2ATH 2F4B 2FVJ 2G0G 2G0H 2GTK 2HFP 2HWQ 2HWR 2I4J 2I4P 2I4Z 2OM9 2P4Y 2POB 2PRG 2Q59 2Q5P 2Q5S 2Q61 2Q6R 2Q6S 2Q8S 2QMV 2VSR 2VST 2VV0 2VV1 2VV2 2VV3 2VV4 2XKW 2YFE 2ZK0 2ZK1 2ZK2 2ZK3 2ZK4 2ZK5 2ZK6 2ZNO 2ZVT 3ADS 3ADT 3ADU 3ADV 3ADW 3ADX 3AN3 3AN4 3B0Q 3B0R 3B1M 3B3K 3BC5 3CDP 3CDS 3CS8 3CWD 3D6D 3DZU 3DZY 3E00 3ET0 3ET3 3FEJ 3FUR 3G9E 3GBK 3H0A 3HO0 3HOD 3IA6 3K8S 3KMG 3LMP 3NOA 3OSI 3OSW 3PBA 3PO9 3PRG 3QT0 3R5N 3R8A 3R8I 3S9S 3SZ1 3T03 3TY0 3U9Q 3V9T 3V9V 3V9Y 3VJH 3VJI 3VN2 3VSO 3VSP 3WJ4 3WJ5 3WMH 3X1H 3X1I 4A4V 4A4W 4CI5 4E4K 4E4Q 4EM9 4EMA 4F9M 4FGY 4HEE 4JAZ 4JL4 4L96 4L98 4O8F 4OJ4 4PRG 4PVU 4PWL 4R2U 4R6S 4XLD 4XTA 4XUM 4Y29
DBJ	BAA18949 BAA23354 BAA32540 BAA36485 BAD20642
EMBL	CAA07224 CAA07225 CAA62152 CAA62153 CAA73032
GB	AAA19971 AAA62110 AAA62277 AAA80314 AAB04028
PIR	JE0279
REF	NP_001019803 NP_001028032 NP_001075617 NP_001094391 NP_001106647
SP	O18924 O18971 O19052 O62807 O88275
TPG	DAA16769
AlphaFold	O18924 O18971 O19052 O62807 O88275

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks