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Ternary complex of human ror gamma ligand binding domain with compound T.

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

PDB: 6A22
Type: protein
Length: 969 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: 9P6
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 70% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nuclear receptor ror-gamma	protein	231	69% helix, 4% strand	P51449
B, H	Nuclear receptor corepressor 2	protein	15	53% helix, 0% strand	Q9Y618
C, E, G	Nuclear receptor ror-gamma	protein	228	71% helix, 4% strand	P51449
D, F	Nuclear receptor corepressor 2	protein	12	83% helix, 0% strand	Q9Y618

Ligands and binding sites

9P6 · 2-[2-[1-~{tert}-butyl-5-(4-methoxyphenyl)pyrazol-4-yl]-1,3-thiazol-4-yl]-~{N}-(oxan-4-ylmethyl)ethanamide · ligand · 4 copies · chains A, C, E, G

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

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	356	0.83	0.92	39	9P6
2	350	0.82	0.91	39	9P6
3	342	0.81	0.90	35	9P6
4	350	0.81	0.90	38	9P6
5	1015	0.80	0.81	100	empty

Interfaces

9 interfaces between chains.

A–B · 754 Å² buried · 4 hydrogen bonds · protein-protein
G–H · 703 Å² buried · 5 hydrogen bonds · protein-protein
E–G · 675 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 639 Å² buried · 3 hydrogen bonds · protein-protein
E–F · 589 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6A22 · Ternary complex of Human ROR gamma Ligand Binding Domain With Compound T. · 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 0.68

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 6A22 · PDBe 6A22 · UniProt P51449 · UniProt Q9Y618

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