Research workbench
The crystal structure of KDM6B bound with H3K27ME3 peptide
Analyse The crystal structure of KDM6B bound with H3K27ME3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EZH
- Type
- protein
- Length
- 928 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 6B; Synthesized methylation peptide
- EC
- 1.14.11.-
- UniProt
- Q5NCY0
- Ligands
- OGA, NI, ZN
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 6B (EC 1.14.11.-) | protein | 455 | 35% helix, 24% strand | Q5NCY0 |
| B | Lysine-specific demethylase 6B (EC 1.14.11.-) | protein | 451 | 35% helix, 24% strand | Q5NCY0 |
| C, D | Synthesized methylation peptide | protein | 11 | 0% helix, 18% strand | — |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, C, B, D
- NI · Nickel (II) ion · metal · 2 copies · chains A, C, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
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 | 898 | 0.81 | 0.83 | 97 | empty |
| 2 | 326 | 0.74 | 0.86 | 55 | OGA |
| 3 | 271 | 0.69 | 0.84 | 40 | NI, OGA |
| 4 | 285 | 0.61 | 0.79 | 33 | empty |
| 5 | 214 | 0.57 | 0.79 | 32 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1041 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 774 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 773 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 4EZH · the crystal structure of KDM6B bound with H3K27me3 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q5NCY0 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 6B (Q5NCY0) · a predicted model of the same protein · chain B 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 Q5NCY0
- Elsewhere: RCSB PDB 4EZH · PDBe 4EZH · UniProt Q5NCY0
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