MolNFT v1 · #124845 · protein

Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with ddt and dde

5KRA · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with ddt and dde”. X-ray diffraction, 2 ligands (6WS, 6WT), 14 pockets (best druggability 0.85). MolNFT v1 #124845 on GenesisL1: 3D…

PDB: 5KRA
Type: protein
Length: 970 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Estrogen receptor; NCOA2
UniProt: P03372
Ligands: 6WS, 6WT
Pockets: 14 · best druggability 0.85

Structure

x-ray diffraction · 6 distinct chains · 69% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Estrogen receptor	protein	226	70% helix, 3% strand	P03372
B	Estrogen receptor	protein	240	70% helix, 4% strand	P03372
C, G, H	NCOA2	protein	10	70% helix, 0% strand	—
D	NCOA2	protein	9	56% helix, 0% strand	—
E	Estrogen receptor	protein	228	69% helix, 4% strand	P03372
F	Estrogen receptor	protein	237	66% helix, 4% strand	P03372

Ligands and binding sites

6WS · 1-[2,2-bis(chloranyl)-1-(4-chlorophenyl)ethenyl]-4-chloranyl-benzene · ligand · 2 copies · chains A, E
6WT · 1-chloranyl-4-[2,2,2-tris(chloranyl)-1-(4-chlorophenyl)ethyl]benzene · ligand · 2 copies · chains B, F

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

Pockets

14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	236	0.85	0.97	30	6WS
2	223	0.85	0.97	33	6WT
3	205	0.84	0.97	24	6WS
4	299	0.83	0.93	38	6WT
5	593	0.68	0.77	58	empty

Interfaces

9 interfaces between chains.

A–B · 1701 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 1685 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 534 Å² buried · 5 hydrogen bonds · protein-protein
E–G · 531 Å² buried · 3 hydrogen bonds · protein-protein
F–H · 528 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5KRA · Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with DDT and… · the same entry in another collection · chain H against H, TM-score 1.00
P03372 · AlphaFold monomer V2.0 prediction for estrogen receptor (P03372) · a predicted model of the same protein · chain E 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 5KRA · PDBe 5KRA · UniProt P03372

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