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Crystal structure of estrogen related receptor-3 (err-gamma) ligand binding domaind with tamoxifen analog GSK5182

Analyse Crystal structure of estrogen related receptor-3 (err-gamma) ligand binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2EWP
Type: protein
Length: 1,106 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Estrogen-related receptor gamma
UniProt: P62508
Ligands: TXF
Pockets: 18 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 66% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Estrogen-related receptor gamma	protein	224	67% helix, 3% strand	P62508
C	Estrogen-related receptor gamma	protein	223	65% helix, 3% strand	P62508
D	Estrogen-related receptor gamma	protein	221	67% helix, 3% strand	P62508
E	Estrogen-related receptor gamma	protein	214	67% helix, 4% strand	P62508

Ligands and binding sites

TXF · (Z)-4-(1-{4-[2-(dimethylamino)ethoxy]phenyl}-5-hydroxy-2-phenylpent-1-enyl)phenol · ligand · 5 copies · chains A, B, C, D, E

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

Pockets

18 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	225	0.81	0.93	28	TXF
2	1171	0.81	0.82	121	empty
3	253	0.79	0.91	35	TXF
4	232	0.79	0.92	28	TXF
5	223	0.79	0.92	28	TXF

Interfaces

4 interfaces between chains.

C–D · 1427 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1377 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 482 Å² buried · 2 hydrogen bonds · protein-protein
C–E · 45 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2EWP · Crystal structure of Estrogen Related Receptor-3 (ERR-gamma) ligand binding domaind with… · the same entry in another collection · chain E against E, TM-score 1.00
P62508 · AlphaFold monomer V2.0 prediction for estrogen-related receptor gamma (P62508) · a predicted model of the same protein · chain D against A, TM-score 0.93

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 P62508
Elsewhere: RCSB PDB 2EWP · PDBe 2EWP · UniProt P62508

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