MolNFT v1 · #99860 · protein

Crystal structure of hera-lbd (Y537S) in complex with benzophenone-2

4MGC · Estrogen receptor: “Crystal structure of hera-lbd (Y537S) in complex with benzophenone-2”. X-ray diffraction, 1 ligand (27M), 7 pockets (best druggability 0.84). MolNFT v1 #99860 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4MGC
Type: protein
Length: 493 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Estrogen receptor; Nuclear receptor coactivator 1
UniProt: P03372, Q15788
Ligands: 27M
Pockets: 7 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 69% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Estrogen receptor	protein	238	71% helix, 4% strand	P03372
B	Estrogen receptor	protein	237	68% helix, 4% strand	P03372
F, G	Nuclear receptor coactivator 1	protein	9	78% helix, 0% strand	Q15788

Ligands and binding sites

27M · bis(2,4-dihydroxyphenyl)methanone · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · 4 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	169	0.84	0.98	22	27M
2	171	0.83	0.97	21	27M
3	80	0.60	0.88	16	empty
4	83	0.59	0.88	17	empty
5	159	0.50	0.78	31	empty

Interfaces

3 interfaces between chains.

A–B · 1705 Å² buried · 24 hydrogen bonds · protein-protein
B–G · 475 Å² buried · 1 hydrogen bond · protein-protein
A–F · 465 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (oxidation).

Compared structures

4MGC · Crystal structure of hERa-LBD (Y537S) in complex with benzophe -2 · the same entry in another collection · chain A against A, TM-score 1.00
P03372 · AlphaFold monomer V2.0 prediction for estrogen receptor (P03372) · a predicted model of the same protein · chain B 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 P03372
Every structure of UniProt Q15788
Elsewhere: RCSB PDB 4MGC · PDBe 4MGC · UniProt P03372 · UniProt Q15788

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.