MolNFT v1 · #139213 · protein

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

5X8Q · Nuclear receptor ror-gamma: “Crystal structure of the mutant human ror gamma ligand binding domain with rockogenin.”. X-ray diffraction, 1 ligand (82R), 11 pockets (best druggability 0.83). MolNFT v1 #139213 on GenesisL1: 3D…

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

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