Research workbench

Nucleosome 3 of the 4X187 nucleosome array containing H1

Analyse Nucleosome 3 of the 4X187 nucleosome array containing H1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7PF4
Type: protein + DNA
Length: 1,102 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-K; DNA (167-mer)
UniProt: Q71DI3, P62805, P04908, O60814
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 6 distinct chains · 63% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
K, O	Histone H3.2	protein	97	68% helix, 4% strand	Q71DI3
L, P	Histone H4	protein	83	61% helix, 6% strand	P62805
M, Q	Histone H2A type 1-B/E	protein	109	50% helix, 5% strand	P04908
N, R	Histone H2B type 1-K	protein	95	72% helix, 4% strand	O60814
J	DNA (167-mer)	dna	167	—	—
I	DNA (167-mer)	dna	167	—	—

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	648	0.82	0.87	86	empty
2	347	0.79	0.89	44	empty
3	241	0.76	0.90	39	empty
4	280	0.75	0.88	35	empty
5	875	0.70	0.76	83	empty

Interfaces

36 interfaces between chains.

J–I · 7579 Å² buried · 666 hydrogen bonds · nucleic-nucleic
M–N · 2647 Å² buried · 25 hydrogen bonds · protein-protein
Q–R · 2586 Å² buried · 36 hydrogen bonds · protein-protein
O–P · 2571 Å² buried · 26 hydrogen bonds · protein-protein
K–L · 2510 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

7PF4 · Nucleosome 3 of the 4x187 nucleosome array containing H1 · the same entry in another collection · chain I against I, TM-score 1.00
Q71DI3 · AlphaFold monomer V2.0 prediction for histone H3.2 (Q71DI3) · a predicted model of the same protein · chain O against A, TM-score 0.97

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 Q71DI3
Every structure of UniProt P62805
Every structure of UniProt P04908
Every structure of UniProt O60814
Elsewhere: RCSB PDB 7PF4 · PDBe 7PF4 · UniProt Q71DI3 · UniProt P62805 · UniProt P04908 · UniProt O60814

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