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Crystal structure of the er alpha ligand binding domain with the agonist ortho-trifluoromethylphenylvinyl estradiol

Analyse Crystal structure of the er alpha ligand binding domain with the agonist… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2P15
Type: protein
Length: 506 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Estrogen receptor; Grip peptide
UniProt: P03372, Q15596
Ligands: EZT
Pockets: 8 · best druggability 0.86

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Estrogen receptor	protein	242	69% helix, 4% strand	P03372
B	Estrogen receptor	protein	242	69% helix, 4% strand	P03372
C	Grip peptide	protein	11	73% helix, 0% strand	Q15596
D	Grip peptide	protein	11	45% helix, 0% strand	Q15596

Ligands and binding sites

EZT · (17beta)-17-{(E)-2-[2-(trifluoromethyl)phenyl]vinyl}estra-1(10),2,4-triene-3,17-diol · 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, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	269	0.86	0.97	31	EZT
2	307	0.85	0.94	33	EZT
3	89	0.62	0.89	17	empty
4	95	0.61	0.88	17	empty
5	332	0.59	0.77	38	empty

Interfaces

3 interfaces between chains.

A–B · 1790 Å² buried · 23 hydrogen bonds · protein-protein
B–D · 538 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 523 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

2P15 · Crystal structure of the ER alpha ligand binding domain with the agonist… · 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 0.98

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 Q15596
Elsewhere: RCSB PDB 2P15 · PDBe 2P15 · UniProt P03372 · UniProt Q15596

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