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Crystal structure of ppar-delta complex

Analyse Crystal structure of ppar-delta complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3D5F
Type: protein
Length: 508 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxisome proliferator-activated receptor delta
UniProt: Q03181
Ligands: L41
Pockets: 5 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 68% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peroxisome proliferator-activated receptor delta	protein	254	70% helix, 5% strand	Q03181
B	Peroxisome proliferator-activated receptor delta	protein	254	67% helix, 5% strand	Q03181

Ligands and binding sites

L41 · {4-[3-(4-acetyl-3-hydroxy-2-propylphenoxy)propoxy]phenoxy}acetic acid · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	473	0.84	0.90	50	L41
2	455	0.83	0.90	51	L41
3	88	0.43	0.79	14	empty
4	68	0.35	0.76	9	empty
5	67	0.32	0.75	11	empty

Interfaces

1 interface between chains.

A–B · 30 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3D5F · Crystal Structure of PPAR-delta complex · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q03181
Elsewhere: RCSB PDB 3D5F · PDBe 3D5F · UniProt Q03181

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