MolNFT v1 · #155500 · protein + DNA

The human telomeric nucleosome displays distinct structural and dynamic properties

6L9H · Histone H3.1: “The human telomeric nucleosome displays distinct structural and dynamic properties”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.79). MolNFT v1 #155500 on GenesisL1: 3D structure, binding sites…

PDB: 6L9H
Type: protein + DNA
Length: 1,043 residues
Chains: 10
Method: x-ray diffraction
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; Human telomeric…
UniProt: P68431, P62805, P04908, O60814
Ligands: MN
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 10 distinct chains · 64% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.1	protein	95	67% helix, 4% strand	P68431
B	Histone H4	protein	87	59% helix, 8% strand	P62805
C	Histone H2A type 1-B/E	protein	103	56% helix, 7% strand	P04908
D	Histone H2B type 1-K	protein	95	74% helix, 4% strand	O60814
E	Histone H3.1	protein	96	66% helix, 4% strand	P68431
F	Histone H4	protein	78	63% helix, 9% strand	P62805
G	Histone H2A type 1-B/E	protein	105	55% helix, 7% strand	P04908
H	Histone H2B type 1-K	protein	94	74% helix, 4% strand	O60814
I	Human telomeric DNA (145-mer) - G-strand	dna	145	—	—
J	Human telomeric DNA (145-mer) - C-strand	dna	145	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 copies · chains I

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	700	0.79	0.83	72	empty
2	399	0.76	0.86	48	empty
3	319	0.75	0.87	40	empty
4	787	0.70	0.77	57	empty
5	824	0.69	0.76	42	empty

Interfaces

35 interfaces between chains.

I–J · 6540 Å² buried · 582 hydrogen bonds · nucleic-nucleic
A–B · 2753 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 2706 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 2590 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 2583 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

6L9H · The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties · the same entry in another collection · chain J against J, TM-score 1.00
O60814 · AlphaFold monomer V2.0 prediction for histone H2B type 1-K (O60814) · a predicted model of the same protein · chain H against A, TM-score 0.88

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 6L9H · PDBe 6L9H · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt O60814

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