Research workbench

169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0

Analyse 169 bp nucleosome, harboring cohesive DNA termini, assembled with linker… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LAB
Type: protein + DNA
Length: 2,416 residues
Chains: 22
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 (169-mer)…
UniProt: P68431, P62805, P04908, P06899, P07305
Ligands: CA, K, CL
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 13 distinct chains · 54% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, K, O	Histone H3.1	protein	98	67% helix, 4% strand	P68431
B	Histone H4	protein	80	63% helix, 9% strand	P62805
C	Histone H2A type 1-B/E	protein	105	57% helix, 7% strand	P04908
D, H, N, R	Histone H2B type 1-J	protein	96	74% helix, 4% strand	P06899
F	Histone H4	protein	85	61% helix, 8% strand	P62805
G, Q	Histone H2A type 1-B/E	protein	103	55% helix, 7% strand	P04908
I, S	DNA (169-mer)	dna	169	—	—
J, T	DNA (169-mer)	dna	169	—	—
L	Histone H4	protein	83	60% helix, 7% strand	P62805
M	Histone H2A type 1-B/E	protein	106	55% helix, 7% strand	P04908
P	Histone H4	protein	86	58% helix, 8% strand	P62805
U	Histone H1.0	protein	104	28% helix, 9% strand	P07305
V	Histone H1.0	protein	109	28% helix, 6% strand	P07305

Ligands and binding sites

CA · Calcium ion · metal · 20 copies · chains C, D, I, J, M, N, S, T
K · Potassium ion · metal · 2 copies · chains C, D, G, M, Q, R
CL · Chloride ion · ion · 2 copies · chains M, N, 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	718	0.80	0.84	65	K
2	709	0.79	0.84	71	empty
3	736	0.79	0.83	74	K
4	411	0.77	0.86	52	empty
5	514	0.76	0.84	49	empty

Interfaces

86 interfaces between chains.

I–J · 7556 Å² buried · 687 hydrogen bonds · nucleic-nucleic
S–T · 7503 Å² buried · 685 hydrogen bonds · nucleic-nucleic
O–P · 2746 Å² buried · 31 hydrogen bonds · protein-protein
G–H · 2671 Å² buried · 25 hydrogen bonds · protein-protein
Q–R · 2666 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

6LAB · 169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0 · 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 P07305
Elsewhere: RCSB PDB 6LAB · PDBe 6LAB · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt P07305

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