Research workbench

Ligand complex of RORg LBD

Analyse Ligand complex of RORg LBD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5G44
Type: protein
Length: 257 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.84
Source: HOMO SAPIENS
Molecule: Nuclear receptor ror-gamma; Rorg
UniProt: P51449
Ligands: I6G, SWX, YTZ, NA
Pockets: 4 · best druggability 0.84

Structure

x-ray diffraction · resolution 1.84 · 2 distinct chains · 71% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nuclear receptor ror-gamma	protein	245	71% helix, 4% strand	P51449
C	Rorg	protein	12	67% helix, 0% strand	—

Ligands and binding sites

I6G · 8-methoxy-2,3-dimethylquinoxalin-5-ol · ligand · chains A
SWX · (4-pyrimidin-5-ylphenyl)methanol · ligand · chains A
YTZ · 4-amino-N-(1,3-thiazol-2-yl)benzenesulfonamide · ligand · chains A
NA · Sodium ion · metal · chains A
DMS · Dimethyl sulfoxide · additive · chains A, C

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	538	0.84	0.90	37	I6G, SWX, YTZ
2	176	0.56	0.80	21	empty
3	78	0.42	0.80	16	NA
4	72	0.32	0.75	12	empty

Interfaces

1 interface between chains.

A–C · 556 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5G44 · Ligand complex of rorg lbd · the same entry in another collection · chain A against A, TM-score 1.00
P51449 · AlphaFold monomer V2.0 prediction for nuclear receptor ror-gamma (P51449) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 5G44 · PDBe 5G44 · UniProt P51449

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