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Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with (E)-4,4''-dihydroxy-3'-((HYDROXYIMINIO)METHYL)-[1,1':2', 1''-terphenyl]-4'-olate

Analyse Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TLG
Type: protein
Length: 483 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Estrogen receptor; Nuclear receptor coactivator 2
UniProt: P03372
Ligands: 7EG
Pockets: 5 · best druggability 0.84

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Estrogen receptor	protein	229	68% helix, 4% strand	P03372
B	Estrogen receptor	protein	236	64% helix, 4% strand	P03372
C, D	Nuclear receptor coactivator 2	protein	9	78% helix, 0% strand	—

Ligands and binding sites

7EG · 2~3~-[(E)-(hydroxyimino)methyl][1~1~,2~1~:2~2~,3~1~-terphenyl]-1~4~,2~4~,3~4~-triol · ligand · 2 copies · chains A, B

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

Pockets

5 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	194	0.84	0.97	23	7EG
2	192	0.84	0.97	21	7EG
3	485	0.67	0.78	61	empty
4	89	0.65	0.90	17	empty
5	90	0.61	0.88	18	empty

Interfaces

3 interfaces between chains.

A–B · 1662 Å² buried · 31 hydrogen bonds · protein-protein
A–C · 506 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 429 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5TLG · Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with… · 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 A 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
Elsewhere: RCSB PDB 5TLG · PDBe 5TLG · UniProt P03372

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