Research workbench

Ligand binding alters the structure and dynamics of nucleosomal DNA

Analyse Ligand binding alters the structure and dynamics of nucleosomal DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1M1A
Type: protein + DNA
Length: 1,059 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Palindromic 146 base pair DNA fragment; Histone H3.2; Histone H4; Histone H2A.1; Histone…
UniProt: P02302, P02304, P06897, P02281
Ligands: PYB, IMT, ABU, BAL, DIB, MN
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 8 distinct chains · 61% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I, J	Palindromic 146 base pair DNA fragment	dna	146	—	—
A	Histone H3.2	protein	99	65% helix, 4% strand	P02302
B	Histone H4	protein	80	61% helix, 8% strand	P02304
C	Histone H2A.1	protein	105	53% helix, 7% strand	P06897
D, H	Histone H2B.1	protein	93	74% helix, 4% strand	P02281
E	Histone H3.2	protein	98	64% helix, 4% strand	P02302
F	Histone H4	protein	93	54% helix, 8% strand	P02304
G	Histone H2A.1	protein	106	55% helix, 6% strand	P06897

Ligands and binding sites

PYB · 4-amino-(1-methylpyrrole)-2-carboxylic acid · ligand · 6 copies · chains J, I
IMT · 4-amino-(1-methylimidazole)-2-carboxylic acid · ligand · 2 copies · chains J
ABU · Gamma-amino-butanoic acid · ligand · chains I, J, E
BAL · Beta-alanine · ligand · chains I, J
DIB · 3-amino-(dimethylpropylamine) · ligand · chains J
MN · Manganese (II) ion · metal · 10 copies · chains I, J, E

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	487	0.77	0.85	50	empty
2	548	0.75	0.83	63	empty
3	311	0.73	0.86	45	empty
4	939	0.71	0.76	82	MN, PYB, ABU
5	789	0.70	0.77	51	empty

Interfaces

34 interfaces between chains.

I–J · 6331 Å² buried · 497 hydrogen bonds · nucleic-nucleic
E–F · 2633 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 2616 Å² buried · 24 hydrogen bonds · protein-protein
G–H · 2580 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2534 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

1M1A · Ligand binding alters the structure and dynamics of nucleosomal DNA · the same entry in another collection · chain H against H, TM-score 1.00
P02302 · AlphaFold monomer V2.0 prediction for histone H3.3C (P02302) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P02302
Every structure of UniProt P02304
Every structure of UniProt P06897
Every structure of UniProt P02281
Elsewhere: RCSB PDB 1M1A · PDBe 1M1A · UniProt P02302 · UniProt P02304 · UniProt P06897 · UniProt P02281

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