Research workbench

Crystal structure of the mutant human ror gamma ligand binding domain with rockogenin.

Analyse Crystal structure of the mutant human ror gamma ligand binding domain with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5X8Q
Type: protein
Length: 970 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclear receptor ror-gamma; Nuclear receptor corepressor 2
UniProt: P51449, Q9Y618
Ligands: 82R
Pockets: 11 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 72% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Nuclear receptor ror-gamma	protein	228	71% helix, 4% strand	P51449
B, H	Nuclear receptor corepressor 2	protein	15	73% helix, 0% strand	Q9Y618
D, F	Nuclear receptor corepressor 2	protein	14	79% helix, 0% strand	Q9Y618

Ligands and binding sites

82R · (1R,2S,4S,5'R,6R,7S,8R,9S,10R,12S,13S,16S,18S)-5',7,9, 13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2, 9}.0^{4,8}.0^{13,18}]icosane-6,2'-oxane]-10,16-diol · ligand · 4 copies · chains A, C, E, G

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1183	0.83	0.84	95	82R
2	378	0.82	0.90	32	82R
3	376	0.81	0.90	31	82R
4	994	0.79	0.81	77	82R
5	752	0.76	0.81	71	empty

Interfaces

9 interfaces between chains.

G–H · 751 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 732 Å² buried · 6 hydrogen bonds · protein-protein
E–F · 719 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 717 Å² buried · 4 hydrogen bonds · protein-protein
E–G · 580 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5X8Q · Crystal Structure of the mutant Human ROR gamma Ligand Binding Domain With rockogenin. · the same entry in another collection · chain H against H, TM-score 1.00
Q9Y618 · AlphaFold monomer V2.0 prediction for nuclear receptor corepressor 2 (Q9Y618) · a predicted model of the same protein · chain D against A, TM-score 0.70

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
Every structure of UniProt Q9Y618
Elsewhere: RCSB PDB 5X8Q · PDBe 5X8Q · UniProt P51449 · UniProt Q9Y618

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.