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Telomeric dinucleosome

Analyse Telomeric dinucleosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7V96
Type: protein + DNA
Length: 2,143 residues
Chains: 18
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (275-mer); Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-K
UniProt: P68431, P62805, P04908, O60814
Pockets: 20 · best druggability 0.78

Structure

electron microscopy · 13 distinct chains · 49% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I	DNA (275-mer)	dna	275	—	—
J	DNA (275-mer)	dna	275	—	—
A	Histone H3.1	protein	100	24% helix, 4% strand	P68431
B, P	Histone H4	protein	84	42% helix, 7% strand	P62805
C	Histone H2A type 1-B/E	protein	109	50% helix, 5% strand	P04908
D, N	Histone H2B type 1-K	protein	99	69% helix, 3% strand	O60814
E, O	Histone H3.1	protein	100	63% helix, 2% strand	P68431
F, L	Histone H4	protein	87	51% helix, 5% strand	P62805
G	Histone H2A type 1-B/E	protein	120	34% helix, 4% strand	P04908
H, R	Histone H2B type 1-K	protein	98	68% helix, 3% strand	O60814
K	Histone H3.1	protein	99	65% helix, 2% strand	P68431
M	Histone H2A type 1-B/E	protein	119	34% helix, 3% strand	P04908
Q	Histone H2A type 1-B/E	protein	110	47% helix, 5% strand	P04908

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	880	0.78	0.81	89	empty
2	1037	0.77	0.79	66	empty
3	799	0.77	0.81	61	empty
4	526	0.75	0.83	51	empty
5	487	0.75	0.84	48	empty

Interfaces

73 interfaces between chains.

I–J · 12864 Å² buried · 1,303 hydrogen bonds · nucleic-nucleic
O–P · 2829 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 2719 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 2713 Å² buried · 18 hydrogen bonds · protein-protein
Q–R · 2703 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

7V96 · Telomeric Dinucleosome · the same entry in another collection · chain K against K, 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 P68431
Every structure of UniProt P62805
Every structure of UniProt P04908
Every structure of UniProt O60814
Elsewhere: RCSB PDB 7V96 · PDBe 7V96 · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt O60814

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