MolNFT v1 · #189321 · protein + DNA

Telomeric tetranucleosome in open state

7VA4 · DNA (539-mer): “Telomeric tetranucleosome in open state”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #189321 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7VA4
Type: protein + DNA
Length: 4,206 residues
Chains: 34
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (539-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 0.83

Structure

electron microscopy · 12 distinct chains · 54% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I	DNA (539-mer)	dna	539	—	—
J	DNA (539-mer)	dna	539	—	—
A, K, S, a	Histone H3.1	protein	95	64% helix, 3% strand	P68431
B, P, T, f	Histone H4	protein	83	58% helix, 7% strand	P62805
C, G, U, Y	Histone H2A type 1-B/E	protein	120	43% helix, 3% strand	P04908
D, N, V, d	Histone H2B type 1-K	protein	95	71% helix, 3% strand	O60814
E, O, W, e	Histone H3.1	protein	96	64% helix, 2% strand	P68431
F, L, X, b	Histone H4	protein	87	56% helix, 3% strand	P62805
H, R, Z, h	Histone H2B type 1-K	protein	94	71% helix, 0% strand	O60814
M	Histone H2A type 1-B/E	protein	119	39% helix, 2% strand	P04908
Q, g	Histone H2A type 1-B/E	protein	110	39% helix, 4% strand	P04908
c	Histone H2A type 1-B/E	protein	109	43% helix, 2% 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	940	0.83	0.85	86	empty
2	815	0.82	0.85	77	empty
3	1022	0.80	0.82	84	empty
4	628	0.80	0.85	66	empty
5	938	0.79	0.82	72	empty

Interfaces

150 interfaces between chains.

I–J · 23724 Å² buried · 1,036 hydrogen bonds · nucleic-nucleic
K–L · 2571 Å² buried · 7 hydrogen bonds · protein-protein
a–b · 2568 Å² buried · 7 hydrogen bonds · protein-protein
O–P · 2548 Å² buried · 22 hydrogen bonds · protein-protein
M–N · 2520 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

7VA4 · Telomeric tetranucleosome in open state · 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 7VA4 · PDBe 7VA4 · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt O60814

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