MolNFT v1 · #155513 · protein + DNA

338 bp di-nucleosome assembled with linker histone H1.X

6L9Z · Histone H3.1: “338 bp di-nucleosome assembled with linker histone H1.X”. X-ray diffraction, 3 ligands (CA, K, CL), 20 pockets (best druggability 0.81). MolNFT v1 #155513 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6L9Z
Type: protein + DNA
Length: 2,328 residues
Chains: 19
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-J; DNA (338-mer)…
UniProt: P68431, P62805, P04908, P06899, Q92522
Ligands: CA, K, CL
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 16 distinct chains · 59% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.1	protein	98	65% helix, 4% strand	P68431
B	Histone H4	protein	84	60% helix, 8% strand	P62805
C	Histone H2A type 1-B/E	protein	112	53% helix, 6% strand	P04908
D, H, R	Histone H2B type 1-J	protein	96	73% helix, 4% strand	P06899
E, O	Histone H3.1	protein	100	63% helix, 4% strand	P68431
F	Histone H4	protein	87	57% helix, 8% strand	P62805
G	Histone H2A type 1-B/E	protein	107	55% helix, 7% strand	P04908
I	DNA (338-mer)	dna	338	—	—
J	DNA (338-mer)	dna	338	—	—
K	Histone H3.1	protein	99	64% helix, 4% strand	P68431
L	Histone H4	protein	85	59% helix, 8% strand	P62805
M	Histone H2A type 1-B/E	protein	111	52% helix, 5% strand	P04908
N	Histone H2B type 1-J	protein	97	72% helix, 4% strand	P06899
P	Histone H4	protein	94	52% helix, 6% strand	P62805
Q	Histone H2A type 1-B/E	protein	106	58% helix, 7% strand	P04908
S	Histone H1X	protein	84	40% helix, 6% strand	Q92522

Ligands and binding sites

CA · Calcium ion · metal · 65 copies · chains D, C, G, I, J, K, M, N, P, Q, R
K · Potassium ion · metal · 10 copies · chains C, G, H, I, J, M, Q, R
CL · Chloride ion · ion · 8 copies · chains A, C, D, J, E, G, H, I, K, M, N, O, Q, R

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	811	0.81	0.84	72	K
2	586	0.78	0.84	58	empty
3	622	0.77	0.83	62	K
4	432	0.77	0.86	53	empty
5	483	0.75	0.84	50	empty

Interfaces

75 interfaces between chains.

I–J · 15467 Å² buried · 1,629 hydrogen bonds · nucleic-nucleic
O–P · 2792 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 2777 Å² buried · 28 hydrogen bonds · protein-protein
E–F · 2712 Å² buried · 30 hydrogen bonds · protein-protein
Q–R · 2658 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

6L9Z · 338 bp di-nucleosome assembled with linker histone H1.X · the same entry in another collection · chain S against S, 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 P06899
Every structure of UniProt Q92522
Elsewhere: RCSB PDB 6L9Z · PDBe 6L9Z · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt Q92522

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