Research workbench
Crystal structure of histone demethylase KDM2A-H3K36ME3 complex with alpha-kg
Analyse Crystal structure of histone demethylase KDM2A-H3K36ME3 complex with alpha-kg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QX8
- Type
- protein
- Length
- 815 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
- 12 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lysine-specific demethylase 2A (EC 1.14.11.27) | protein | 329 | 37% helix, 22% 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 | 11 | 0% helix, 9% strand | P84228 |
| F | Histone H3.2 | protein | 10 | 0% helix, 10% 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, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.77 | 0.97 | 31 | NI, AKG |
| 2 | 97 | 0.77 | 0.97 | 28 | NI, AKG |
| 3 | 54 | 0.58 | 0.90 | 19 | empty |
| 4 | 272 | 0.50 | 0.74 | 43 | empty |
| 5 | 188 | 0.50 | 0.77 | 29 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2098 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2054 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 942 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 897 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 384 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 4QX8 · Crystal structure of histone demethylase kdm2a-h3k36me3 complex with alpha-kg · 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 E against A, TM-score 0.37
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 4QX8 · PDBe 4QX8 · UniProt F6YRW4 · UniProt P84228
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