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Crystal structure of histone demethylase KDM2A-H3K36ME3 with nog

Analyse Crystal structure of histone demethylase KDM2A-H3K36ME3 with nog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4QXB
Type: protein
Length: 816 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine-specific demethylase 2A; Histone H3.2
EC: 1.14.11.27
UniProt: F6YRW4, P84228
Ligands: OGA, NI
Pockets: 13 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Lysine-specific demethylase 2A (EC 1.14.11.27)	protein	329	37% helix, 23% strand	F6YRW4
B, D	Lysine-specific demethylase 2A (EC 1.14.11.27)	protein	68	50% helix, 1% strand	F6YRW4
E	Histone H3.2	protein	13	0% helix, 8% strand	P84228
F	Histone H3.2	protein	9	0% helix, 11% strand	P84228

Ligands and binding sites

OGA · N-oxalylglycine · ligand · 2 copies · chains A, E, C, F
NI · Nickel (II) ion · metal · 2 copies · chains A, C

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

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	100	0.78	0.97	31	OGA
2	160	0.75	0.92	33	OGA, NI
3	824	0.67	0.74	62	empty
4	80	0.53	0.85	21	empty
5	74	0.51	0.84	22	empty

Interfaces

7 interfaces between chains.

A–B · 2020 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 2010 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 1037 Å² buried · 13 hydrogen bonds · protein-protein
C–F · 892 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 286 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (methylation).

Compared structures

4QXB · crystal structure of histone demethylase KDM2A-H3K36ME3 with NOG · the same entry in another collection · chain F against F, TM-score 1.00
P84228 · AlphaFold monomer V2.0 prediction for histone H3.2 (P84228) · a predicted model of the same protein · chain F against A, TM-score 0.42

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 F6YRW4
Every structure of UniProt P84228
Elsewhere: RCSB PDB 4QXB · PDBe 4QXB · UniProt F6YRW4 · UniProt P84228

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