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Crystal structure of the orphan nuclear receptor ROR(GAMMA)T ligand- binding domain in complex with small molecule ligand

Analyse Crystal structure of the orphan nuclear receptor ROR(GAMMA)T ligand- binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NIE
Type: protein
Length: 509 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclear receptor ror-gamma; Peptide from nuclear receptor coactivator 2
UniProt: P51449, E7EWM1
Ligands: NBH, DMX
Pockets: 8 · best druggability 0.90

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nuclear receptor ror-gamma	protein	245	72% helix, 4% strand	P51449
C	Peptide from nuclear receptor coactivator 2	protein	9	78% helix, 0% strand	E7EWM1
D	Peptide from nuclear receptor coactivator 2	protein	10	70% helix, 0% strand	E7EWM1

Ligands and binding sites

NBH · N-(4-{[benzyl(propyl)amino]methyl}phenyl)-2-[4-(ethylsulfonyl)phenyl]acetamide · ligand · 2 copies · chains A, B
DMX · 3-[benzyl(dimethyl)ammonio]propane-1-sulfonate · ligand · 2 copies · chains A, B

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

Pockets

8 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	1194	0.90	0.91	95	NBH
2	277	0.54	0.75	32	empty
3	193	0.49	0.76	21	empty
4	144	0.47	0.77	20	DMX
5	112	0.41	0.76	13	DMX

Interfaces

5 interfaces between chains.

A–B · 964 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 530 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 487 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 219 Å² buried · 1 hydrogen bond · protein-protein
A–C · 211 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4NIE · Crystal structure of the orphan nuclear receptor ROR(gamma)t ligand-binding domain in… · 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
Every structure of UniProt E7EWM1
Elsewhere: RCSB PDB 4NIE · PDBe 4NIE · UniProt P51449 · UniProt E7EWM1

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