MolNFT v1 · #168579 · protein + DNA

PRC2-AEBP2-JARID2 bound to H2AK119UB1 nucleosome

6WKR · Ubiquitin: “PRC2-AEBP2-JARID2 bound to H2AK119UB1 nucleosome”. Electron microscopy, 3 ligands (SAH, MG, ZN), 20 pockets (best druggability 0.86). MolNFT v1 #168579 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6WKR
Type: protein + DNA
Length: 3,331 residues
Chains: 18
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin; Polycomb protein SUZ12; Polycomb protein eed; Histone-binding protein RBBP4…
EC: 2.1.1.356
UniProt: P0CG48, Q15022, O75530, Q09028, Q15910, Q92833, Q6ZN18, P84233, P62799, P06897, P02281
Ligands: SAH, MG, ZN
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 16 distinct chains · 32% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T, F	Ubiquitin	protein	76	25% helix, 34% strand	P0CG48
A	Polycomb protein SUZ12	protein	439	31% helix, 19% strand	Q15022
L	Polycomb protein eed	protein	362	3% helix, 44% strand	O75530
N	Histone-binding protein RBBP4	protein	395	9% helix, 35% strand	Q09028
C	Histone-lysine N-methyltransferase EZH2 (EC 2.1.1.356)	protein	606	33% helix, 11% strand	Q15910
B	Protein jumonji	protein	42	29% helix, 0% strand	Q92833
P	Zinc finger protein AEBP2	protein	193	34% helix, 18% strand	Q6ZN18
H	DNA (314-mer)	dna	314	—	—
I	Histone H3.2	protein	117	55% helix, 5% strand	P84233
J	Histone H4	protein	83	63% helix, 6% strand	P62799
K, R	Histone H2A type 1	protein	108	52% helix, 4% strand	P06897
M	Histone H2B 1.1	protein	95	69% helix, 2% strand	P02281
O	Histone H3.2	protein	99	61% helix, 1% strand	P84233
Q	Histone H4	protein	87	59% helix, 3% strand	P62799
S	Histone H2B 1.1	protein	96	69% helix, 4% strand	P02281
E	Protein jumonji	protein	35	54% helix, 0% strand	Q92833

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · chains C
MG · Magnesium ion · metal · chains A
ZN · Zinc ion · metal · chains P

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	734	0.86	0.89	56	empty
2	1004	0.86	0.86	115	empty
3	795	0.85	0.87	101	empty
4	969	0.84	0.86	95	SAH
5	937	0.83	0.85	88	empty

Interfaces

52 interfaces between chains.

A–N · 3636 Å² buried · 60 hydrogen bonds · protein-protein
L–C · 3286 Å² buried · 40 hydrogen bonds · protein-protein
A–C · 2807 Å² buried · 18 hydrogen bonds · protein-protein
R–S · 2580 Å² buried · 21 hydrogen bonds · protein-protein
K–M · 2537 Å² buried · 26 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 1 modified (disulfide, methylation).

Compared structures

6WKR · PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome · the same entry in another collection · chain E against E, 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 P0CG48
Every structure of UniProt Q15022
Every structure of UniProt O75530
Every structure of UniProt Q09028
Every structure of UniProt Q15910
Every structure of UniProt Q92833
Every structure of UniProt Q6ZN18
Every structure of UniProt P84233
Every structure of UniProt P62799
Every structure of UniProt P06897
Every structure of UniProt P02281
Elsewhere: RCSB PDB 6WKR · PDBe 6WKR · UniProt P0CG48 · UniProt Q15022 · UniProt O75530 · UniProt Q09028 · UniProt Q15910 · UniProt Q92833 · UniProt Q6ZN18 · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281

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