MolNFT v1 · #29498 · protein

Crystal structure of estrogen receptor beta complexed with 3-bromo-6-hydroxy-2-(4-hydroxy-phenyl)-inden-1-one

1ZAF: “Crystal structure of estrogen receptor beta complexed with 3-bromo-6-hydroxy-2-(4-hydroxy-phenyl)-inden-1-one”. X-ray diffraction, 1 ligand (789), 7 pockets (best druggability 0.83). MolNFT v1 #29498 on GenesisL1: 3D structure…

PDB: 1ZAF
Type: protein
Length: 482 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Estrogen receptor beta; Nuclear receptor coactivator 1
EC: 2.3.1.48
UniProt: Q92731, Q15788
Ligands: 789
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 68% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Estrogen receptor beta	protein	228	70% helix, 3% strand	Q92731
C, D	Nuclear receptor coactivator 1 (EC 2.3.1.48)	protein	13	46% helix, 0% strand	Q15788

Ligands and binding sites

789 · 3-bromo-6-hydroxy-2-(4-hydroxyphenyl)-1H-inden-1-one · ligand · 2 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	149	0.83	0.98	21	789
2	160	0.81	0.96	21	789
3	81	0.67	0.93	21	empty
4	551	0.65	0.76	49	empty
5	133	0.62	0.86	23	empty

Interfaces

3 interfaces between chains.

A–B · 1347 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 578 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 513 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1ZAF · Crystal structure of estrogen receptor beta complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
Q92731 · AlphaFold monomer V2.0 prediction for estrogen receptor beta (Q92731) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q92731
Every structure of UniProt Q15788
Elsewhere: RCSB PDB 1ZAF · PDBe 1ZAF · UniProt Q92731 · UniProt Q15788

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