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X-ray co-structure of nuclear receptor ror-gammat ligand binding domain with an agonist and SRC2 peptide

Analyse X-ray co-structure of nuclear receptor ror-gammat ligand binding domain with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VB7
Type: protein
Length: 259 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclear receptor ror-gamma, SRC2 chimera
UniProt: P51449
Ligands: 921, NA
Pockets: 4 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 73% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nuclear receptor ror-gamma, SRC2 chimera	protein	259	73% helix, 4% strand	P51449

Ligands and binding sites

921 · N-methyl-N'-(3-methylbut-2-en-1-yl)-N'-(3-phenoxyphenyl)-N-[trans-4-(pyridin-4-yl) cyclohexyl]urea · ligand · chains A
NA · Sodium ion · metal · chains A

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

Pockets

4 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	404	0.83	0.91	38	921
2	149	0.53	0.80	20	empty
3	65	0.40	0.80	13	NA
4	82	0.33	0.74	18	empty

Compared structures

5VB7 · X-ray co-structure of nuclear receptor ROR-gammat Ligand Binding Domain with an agonist… · 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 P51449
Elsewhere: RCSB PDB 5VB7 · PDBe 5VB7 · UniProt P51449

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