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Crystal structure of an active polycomb repressive complex 2 in the stimulated state

Analyse Crystal structure of an active polycomb repressive complex 2 in the stimulated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KJH
Type: protein
Length: 1,296 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative polycomb protein eed; Putative uncharacterized PROTEIN,ZINC finger domain…
UniProt: G0S8H7, G0SDW4, G0RYC6
Ligands: SAH, ZN
Pockets: 16 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 27% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative polycomb protein eed	protein	481	9% helix, 39% strand	G0S8H7
B	Putative uncharacterized PROTEIN,ZINC finger domain- containing protein	protein	807	37% helix, 13% strand	G0SDW4, G0RYC6
D	Peptide H3K27ME3	protein	8	0% helix, 13% strand	—

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · chains B
ZN · Zinc ion · metal · 8 copies · chains B

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

Pockets

16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	692	0.86	0.90	59	empty
2	470	0.83	0.90	69	empty
3	614	0.83	0.88	65	empty
4	939	0.75	0.78	72	SAH
5	514	0.74	0.82	76	empty

Interfaces

3 interfaces between chains.

A–B · 5643 Å² buried · 77 hydrogen bonds · protein-protein
A–D · 532 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 239 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (methylation).

Compared structures

5KJH · Crystal structure of an active polycomb repressive complex 2 in the stimulated state · the same entry in another collection · chain A 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 G0S8H7
Every structure of UniProt G0SDW4
Every structure of UniProt G0RYC6
Elsewhere: RCSB PDB 5KJH · PDBe 5KJH · UniProt G0S8H7 · UniProt G0SDW4 · UniProt G0RYC6

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