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

Analyse Crystal structure of hera-lbd (Y537S) in complex with ferutinine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4MG7
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: 27H
Pockets: 7 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 68% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Estrogen receptor	protein	239	69% helix, 4% strand	P03372
B	Estrogen receptor	protein	235	67% helix, 4% strand	P03372
C	Nuclear receptor coactivator 1	protein	9	78% helix, 0% strand	Q15788
D	Nuclear receptor coactivator 1	protein	10	70% helix, 0% strand	Q15788

Ligands and binding sites

27H · ferutinine · ligand · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 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	251	0.86	0.97	25	27H
2	266	0.84	0.95	25	27H
3	81	0.62	0.90	16	empty
4	84	0.59	0.88	16	empty
5	173	0.52	0.78	25	empty

Interfaces

3 interfaces between chains.

A–B · 1715 Å² buried · 29 hydrogen bonds · protein-protein
A–C · 514 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 458 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (oxidation).

Compared structures

4MG7 · Crystal structure of hERa-LBD (Y537S) in complex with ferutinine · 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 Q15788
Elsewhere: RCSB PDB 4MG7 · PDBe 4MG7 · UniProt P03372 · UniProt Q15788

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