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1.6A crystal structure of the non-histone domain of the histone variant MACROH2A1.1.

Analyse 1.6A crystal structure of the non-histone domain of the histone variant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YD9
Type: protein
Length: 750 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Core histone macro-H2A.1
UniProt: Q02874
Ligands: AU
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Core histone macro-H2A.1	protein	188	39% helix, 20% strand	Q02874
B	Core histone macro-H2A.1	protein	187	39% helix, 21% strand	Q02874
C	Core histone macro-H2A.1	protein	187	40% helix, 21% strand	Q02874

Ligands and binding sites

AU · Gold ion · metal · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	945	0.78	0.81	85	AU
2	283	0.59	0.78	35	empty
3	96	0.58	0.86	21	empty
4	230	0.58	0.79	31	empty
5	139	0.55	0.82	27	empty

Interfaces

6 interfaces between chains.

A–D · 341 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 297 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 240 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 198 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 195 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1YD9 · 1.6A Crystal Structure of the Non-Histone Domain of the Histone Variant MacroH2A1.1. · the same entry in another collection · chain A against A, TM-score 1.00
Q02874 · AlphaFold monomer V2.0 prediction for core histone macro-H2A.1 (Q02874) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q02874
Elsewhere: RCSB PDB 1YD9 · PDBe 1YD9 · UniProt Q02874

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