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Cryo-EM structure of RBBP5 bound to the nucleosome

Analyse Cryo-EM structure of RBBP5 bound to the nucleosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PWX
Type: protein + DNA
Length: 1,366 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinoblastoma-binding protein 5; Histone H3.2; Histone H4; Histone H2A type 1; Histone…
UniProt: Q15291, P84233, P62799, P06897, P02281
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 7 distinct chains · 36% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Retinoblastoma-binding protein 5	protein	314	2% helix, 47% strand	Q15291
G, K	Histone H3.2	protein	98	64% helix, 4% strand	P84233
H, L	Histone H4	protein	82	62% helix, 6% strand	P62799
I, M	Histone H2A type 1	protein	107	53% helix, 5% strand	P06897
J, N	Histone H2B 1.1	protein	93	74% helix, 4% strand	P02281
O	DNA (146-mer)	dna	146	—	—
P	DNA (146-mer)	dna	146	—	—

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	953	0.85	0.87	116	empty
2	798	0.84	0.87	58	empty
3	956	0.80	0.82	71	empty
4	283	0.75	0.88	39	empty
5	256	0.70	0.86	33	empty

Interfaces

41 interfaces between chains.

O–P · 6500 Å² buried · 587 hydrogen bonds · nucleic-nucleic
M–N · 2551 Å² buried · 20 hydrogen bonds · protein-protein
G–H · 2532 Å² buried · 22 hydrogen bonds · protein-protein
K–L · 2527 Å² buried · 22 hydrogen bonds · protein-protein
I–J · 2495 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

6PWX · Cryo-EM structure of RbBP5 bound to the nucleosome · the same entry in another collection · chain L against L, TM-score 1.00
Q15291 · AlphaFold monomer V2.0 prediction for retinoblastoma-binding protein 5 (Q15291) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q15291
Every structure of UniProt P84233
Every structure of UniProt P62799
Every structure of UniProt P06897
Every structure of UniProt P02281
Elsewhere: RCSB PDB 6PWX · PDBe 6PWX · UniProt Q15291 · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281

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