Research workbench
Crystal structure of histone demethylase NO66
Analyse Crystal structure of histone demethylase NO66 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E4H
- Type
- protein
- Length
- 1,825 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase NO66
- EC
- 1.14.11.27
- UniProt
- Q9H6W3
- Ligands
- FE
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase NO66 (EC 1.14.11.27) | protein | 455 | 38% helix, 22% strand | Q9H6W3 |
| B | Lysine-specific demethylase NO66 (EC 1.14.11.27) | protein | 458 | 38% helix, 22% strand | Q9H6W3 |
| C | Lysine-specific demethylase NO66 (EC 1.14.11.27) | protein | 455 | 38% helix, 21% strand | Q9H6W3 |
| D | Lysine-specific demethylase NO66 (EC 1.14.11.27) | protein | 457 | 38% helix, 22% strand | Q9H6W3 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains A
- GOL · Glycerol · additive · chains B, C
- PEG · Di(hydroxyethyl)ether · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.74 | 0.79 | 89 | empty |
| 2 | 308 | 0.73 | 0.86 | 50 | empty |
| 3 | 259 | 0.72 | 0.86 | 34 | empty |
| 4 | 283 | 0.71 | 0.85 | 47 | empty |
| 5 | 555 | 0.71 | 0.80 | 72 | FE, GOL |
Interfaces
4 interfaces between chains.
- B–C · 3356 Ų buried · 56 hydrogen bonds · protein-protein
- A–D · 3273 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 1269 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1220 Ų buried · 6 hydrogen bonds · protein-protein
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 Q9H6W3
- Elsewhere: RCSB PDB 4E4H · PDBe 4E4H · UniProt Q9H6W3
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