MolNFT v1 · #105188 · protein
Crystal structure of histone demethylase KDM2A-H3K36ME2 with alpha-kg
4QX7 · Lysine-specific demethylase 2A: “Crystal structure of histone demethylase KDM2A-H3K36ME2 with alpha-kg”. X-ray diffraction, 2 ligands (AKG, NI), 9 pockets (best druggability 0.74). MolNFT v1 #105188 on GenesisL1: 3D structure…
- PDB
- 4QX7
- 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
- AKG, NI
- Pockets
- 9 · best druggability 0.74
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
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, E, C, F
- NI · Nickel (II) ion · metal · 2 copies · chains A, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.74 | 0.92 | 32 | AKG |
| 2 | 61 | 0.73 | 0.98 | 19 | empty |
| 3 | 1021 | 0.69 | 0.74 | 86 | empty |
| 4 | 74 | 0.57 | 0.88 | 22 | empty |
| 5 | 129 | 0.42 | 0.75 | 22 | empty |
Interfaces
7 interfaces between chains.
- C–D · 2072 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2037 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 1039 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 885 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 262 Ų buried · 3 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 4QX7 · PDBe 4QX7 · UniProt F6YRW4 · UniProt P84228
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