MolNFT v1 · #129900 · protein
The structural basis of the histone demethylase KDM6B histone 3 lysine 27 specificity
5OY3 · Lysine-specific demethylase 6B: “The structural basis of the histone demethylase KDM6B histone 3 lysine 27 specificity”. X-ray diffraction, 3 ligands (AKG, FE, ZN), 7 pockets (best druggability 0.76). MolNFT v1 #129900 on GenesisL1…
- PDB
- 5OY3
- Type
- protein
- Length
- 467 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 6B; Histone 3 peptide H3(17-33)A21M
- EC
- 1.14.11.-
- UniProt
- O15054
- Ligands
- AKG, FE, ZN
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 6B (EC 1.14.11.-) | protein | 450 | 35% helix, 23% strand | O15054 |
| B | Histone 3 peptide H3(17-33)A21M | protein | 17 | 0% helix, 24% strand | — |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- FE · Fe (III) ion · metal · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 8 copies · chains A
- TBU · Tertiary-butyl alcohol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.76 | 0.88 | 37 | FE, AKG |
| 2 | 134 | 0.54 | 0.82 | 22 | empty |
| 3 | 117 | 0.42 | 0.76 | 19 | empty |
| 4 | 106 | 0.38 | 0.75 | 19 | EDO |
| 5 | 64 | 0.38 | 0.79 | 17 | TBU |
Interfaces
1 interface between chains.
- A–B · 1280 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5OY3 · The structural basis of the histone demethylase KDM6B histone 3 lysine 27 specificity · the same entry in another collection · chain A against A, TM-score 1.00
- O15054 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 6B (O15054) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O15054
- Elsewhere: RCSB PDB 5OY3 · PDBe 5OY3 · UniProt O15054
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