MolNFT v1 · #101916 · protein
Zinc fingers of KDM2B
4O64 · Lysine-specific demethylase 2B: “Zinc fingers of KDM2B”. X-ray diffraction, 2 ligands (ZN, UNX), 1 pocket (best druggability 0.28). MolNFT v1 #101916 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4O64
- Type
- protein
- Length
- 347 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 2B
- UniProt
- Q8NHM5
- Ligands
- ZN, UNX
- Pockets
- 1 · best druggability 0.28
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lysine-specific demethylase 2B | protein | 116 | 23% helix, 10% strand | Q8NHM5 |
| B | Lysine-specific demethylase 2B | protein | 115 | 21% helix, 10% strand | Q8NHM5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C
- UNX · Unknown atom or ion · ion · 14 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.28 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 243 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 114 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 87 Ų buried · 1 hydrogen bond · 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 Q8NHM5
- Elsewhere: RCSB PDB 4O64 · PDBe 4O64 · UniProt Q8NHM5
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