MolNFT v1 · #105569 · protein + DNA

Crystal structure of the RING1B/BMI1/UBCH5C PRC1 ubiquitylation module bound to the nucleosome core particle

4R8P · Histone H3.2: “Crystal structure of the RING1B/BMI1/UBCH5C PRC1 ubiquitylation module bound to the nucleosome core particle”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.82). MolNFT v1 #105569 on GenesisL1: 3D…

PDB: 4R8P
Type: protein + DNA
Length: 1,762 residues
Chains: 14
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (147-mer); Polycomb complex…
EC: 6.3.2.-, 6.3.2.19
UniProt: P84233, P62799, Q6AZJ8, P02281, P35226, Q99496, P61077
Ligands: ZN
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 13 distinct chains · 45% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	98	62% helix, 4% strand	P84233
B	Histone H4	protein	86	58% helix, 8% strand	P62799
C	Histone H2A	protein	104	55% helix, 7% strand	Q6AZJ8
D, H	Histone H2B 1.1	protein	95	73% helix, 4% strand	P02281
E	Histone H3.2	protein	97	65% helix, 4% strand	P84233
F	Histone H4	protein	82	62% helix, 9% strand	P62799
G	Histone H2A	protein	107	52% helix, 7% strand	Q6AZJ8
I	DNA (147-mer)	dna	144	—	—
J	DNA (147-mer)	dna	145	—	—
K	Polycomb complex protein bmi-1	protein	105	38% helix, 18% strand	P35226
L	E3 ubiquitin-protein ligase RING2, ubiquitin-conjugating enzyme E2 D3 (EC 6.3.2.-, 6.3.2.19)	protein	254	22% helix, 17% strand	Q99496, P61077
M	Polycomb complex protein bmi-1	protein	97	34% helix, 19% strand	P35226
N	E3 ubiquitin-protein ligase RING2, ubiquitin-conjugating enzyme E2 D3 (EC 6.3.2.-, 6.3.2.19)	protein	253	32% helix, 17% strand	Q99496, P61077

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains K, L, M, N

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	1088	0.82	0.83	109	empty
2	870	0.78	0.81	79	empty
3	390	0.74	0.85	44	empty
4	345	0.74	0.86	41	empty
5	884	0.74	0.78	99	empty

Interfaces

54 interfaces between chains.

I–J · 6592 Å² buried · 524 hydrogen bonds · nucleic-nucleic
A–B · 2577 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 2545 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 2533 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 2491 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

4R8P · Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the… · the same entry in another collection · chain N against N, 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 P84233
Every structure of UniProt P62799
Every structure of UniProt Q6AZJ8
Every structure of UniProt P02281
Every structure of UniProt P35226
Every structure of UniProt Q99496
Every structure of UniProt P61077
Elsewhere: RCSB PDB 4R8P · PDBe 4R8P · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt P35226 · UniProt Q99496 · UniProt P61077

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