MolNFT v1 · #189309 · protein + DNA

Telomeric trinucleosome

7V9J · Histone H3.1: “Telomeric trinucleosome”. Electron microscopy, 20 pockets (best druggability 0.80). MolNFT v1 #189309 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7V9J
Type: protein + DNA
Length: 3,174 residues
Chains: 26
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-K; DNA (408-mer)
UniProt: P68431, P62805, P04908, O60814
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 12 distinct chains · 58% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, K, O, S, W	Histone H3.1	protein	100	61% helix, 2% strand	P68431
B, P	Histone H4	protein	84	61% helix, 5% strand	P62805
C, U	Histone H2A type 1-B/E	protein	109	53% helix, 4% strand	P04908
D, N, V	Histone H2B type 1-K	protein	99	70% helix, 2% strand	O60814
F, L	Histone H4	protein	87	59% helix, 6% strand	P62805
G	Histone H2A type 1-B/E	protein	120	48% helix, 3% strand	P04908
H, R, Z	Histone H2B type 1-K	protein	98	70% helix, 2% strand	O60814
M	Histone H2A type 1-B/E	protein	119	49% helix, 3% strand	P04908
Q, Y	Histone H2A type 1-B/E	protein	110	53% helix, 5% strand	P04908
T, X	Histone H4	protein	83	61% helix, 5% strand	P62805
I	DNA (408-mer)	dna	399	—	—
J	DNA (408-mer)	dna	399	—	—

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	1000	0.80	0.82	73	empty
2	1126	0.79	0.81	91	empty
3	922	0.77	0.80	83	empty
4	728	0.77	0.81	65	empty
5	972	0.76	0.79	80	empty

Interfaces

112 interfaces between chains.

I–J · 16890 Å² buried · 1,093 hydrogen bonds · nucleic-nucleic
O–P · 2662 Å² buried · 18 hydrogen bonds · protein-protein
K–L · 2600 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 2592 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 2562 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

7V9J · Telomeric trinucleosome · the same entry in another collection · chain M against M, 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 7V9J · PDBe 7V9J · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt O60814

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