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Crystal Structure of EED in Complex with UNC4859

Analyse Crystal Structure of EED in Complex with UNC4859 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TTW
Type: protein
Length: 728 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.74
Source: Homo sapiens; SYNTHETIC CONSTRUCT
Molecule: Polycomb protein EED; UNC4859
UniProt: O75530
Ligands: UNX, SO4
Pockets: 9 · best druggability 0.76

Structure

x-ray diffraction · resolution 1.74 · 3 distinct chains · 5% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polycomb protein EED	protein	360	7% helix, 48% strand	O75530
B, D	UNC4859	protein	5	0% helix, 0% strand	—
C	Polycomb protein EED	protein	358	4% helix, 47% strand	O75530

Ligands and binding sites

UNX · Unknown atom or ion · ion · 22 copies · chains A, C, D
SO4 · Sulfate ion · ion · 2 copies · chains A, C

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

Pockets

9 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	0.76	0.84	38	empty
2	438	0.76	0.85	43	empty
3	99	0.75	0.96	21	empty
4	175	0.42	0.74	32	UNX
5	140	0.41	0.75	27	empty

Interfaces

3 interfaces between chains.

A–C · 852 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 433 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 430 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (methylation, nonstandard).

Compared structures

5TTW · Crystal structure of eed in complex with UNC4859 · 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 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 O75530
Elsewhere: RCSB PDB 5TTW · PDBe 5TTW · UniProt O75530

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