MolNFT v1 · #180387 · protein

Crystal structure of human eed

7KXT · Polycomb protein eed: “Crystal structure of human eed”. X-ray diffraction, 2 ligands (XB7, UNX), 6 pockets (best druggability 0.78). MolNFT v1 #180387 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7KXT
Type: protein
Length: 724 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polycomb protein eed
UniProt: O75530
Ligands: XB7, UNX
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polycomb protein eed	protein	365	7% helix, 46% strand	O75530
B	Polycomb protein eed	protein	359	7% helix, 46% strand	O75530

Ligands and binding sites

XB7 · 1-[(4-fluorophenyl)methyl]-N-{1-[2-(4-methoxyphenyl) ethyl]piperidin-4-yl}-1H-benzimidazol-2-amine · ligand · 2 copies · chains A, B
UNX · Unknown atom or ion · ion · 52 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	483	0.78	0.86	39	UNX
2	454	0.78	0.86	36	UNX
3	579	0.66	0.76	50	XB7, UNX
4	93	0.36	0.75	18	UNX
5	76	0.32	0.74	18	UNX

Interfaces

1 interface between chains.

A–B · 309 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

7KXT · Crystal structure of human EED · the same entry in another collection · chain A against A, TM-score 1.00
O75530 · AlphaFold monomer V2.0 prediction for polycomb protein eed (O75530) · a predicted model of the same protein · chain B against A, TM-score 1.00

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 O75530
Elsewhere: RCSB PDB 7KXT · PDBe 7KXT · UniProt O75530

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