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Structure of the chromatin remodelling enzyme CHD1 bound to a ubiquitinylated nucleosome

Analyse Structure of the chromatin remodelling enzyme CHD1 bound to a ubiquitinylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6FTX
Type: protein + DNA
Length: 2,127 residues
Chains: 13
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3; Histone H4; Histone H2A type 1; Histone H2B; Histone H3.3C; DNA (159-mer)…
UniProt: S4RAZ3, P62799, P06897, F6TNY0, P02302, P0CG47
Ligands: BEF, ADP
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 12 distinct chains · 47% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3	protein	97	66% helix, 2% strand	S4RAZ3
B	Histone H4	protein	83	61% helix, 5% strand	P62799
C	Histone H2A type 1	protein	103	54% helix, 4% strand	P06897
D	Histone H2B	protein	95	69% helix, 2% strand	F6TNY0
E	Histone H3.3C	protein	110	53% helix, 2% strand	P02302
F	Histone H4	protein	92	53% helix, 4% strand	P62799
G	Histone H2A type 1	protein	105	51% helix, 3% strand	P06897
H	Histone H2B	protein	93	73% helix, 1% strand	F6TNY0
I	DNA (159-mer)	dna	159	—	—
J	DNA (160-mer)	dna	160	—	—
N, O	Polyubiquitin-B	protein	76	14% helix, 22% strand	P0CG47
W	Chromatin-remodeling ATPase	protein	878	39% helix, 10% strand	—

Ligands and binding sites

BEF · Beryllium trifluoride ion · ligand · chains W
ADP · Adenosine-5'-diphosphate · ligand · chains W

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	668	0.87	0.91	80	BEF
2	287	0.82	0.93	61	empty
3	547	0.81	0.87	50	empty
4	120	0.79	0.96	33	empty
5	504	0.74	0.83	58	empty

Interfaces

45 interfaces between chains.

I–J · 7215 Å² buried · 619 hydrogen bonds · nucleic-nucleic
E–F · 2485 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 2431 Å² buried · 13 hydrogen bonds · protein-protein
G–H · 2412 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 2389 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

6FTX · Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome · the same entry in another collection · chain W against W, 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 S4RAZ3
Every structure of UniProt P62799
Every structure of UniProt P06897
Every structure of UniProt F6TNY0
Every structure of UniProt P02302
Every structure of UniProt P0CG47
Elsewhere: RCSB PDB 6FTX · PDBe 6FTX · UniProt S4RAZ3 · UniProt P62799 · UniProt P06897 · UniProt F6TNY0 · UniProt P02302 · UniProt P0CG47

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