MolNFT v1 · #105191 · protein
Crystal structure of histone demethylase KDM2A-H3K36ME3 with nog
4QXB · Lysine-specific demethylase 2A: “Crystal structure of histone demethylase KDM2A-H3K36ME3 with nog”. X-ray diffraction, 2 ligands (OGA, NI), 13 pockets (best druggability 0.78). MolNFT v1 #105191 on GenesisL1: 3D structure, binding…
- 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.
| Volume (ų) | 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 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2010 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1037 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 892 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 286 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
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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