Research workbench
Crystal structure of jmjc domain of human histone 3 lysine-specific demethylase 3B (KDM3B)
Analyse Crystal structure of jmjc domain of human histone 3 lysine-specific demethylase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C8D
- Type
- protein
- Length
- 332 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 3B
- EC
- 1.14.11.-
- UniProt
- Q7LBC6
- Ligands
- OGA, MN, CL
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 3B (EC 1.14.11.-) | protein | 332 | 36% helix, 24% strand | Q7LBC6 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- CL · Chloride ion · ion · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.53 | 0.88 | 18 | ACT |
| 2 | 55 | 0.49 | 0.86 | 16 | MN, OGA |
| 3 | 98 | 0.45 | 0.79 | 20 | empty |
| 4 | 79 | 0.33 | 0.74 | 22 | empty |
| 5 | 72 | 0.31 | 0.74 | 19 | empty |
Compared structures
- 4C8D · Crystal structure of JmjC domain of human histone 3 Lysine-specific demethylase 3B (KDM3B) · the same entry in another collection · chain A against A, TM-score 1.00
- Q7LBC6 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 3B (Q7LBC6) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q7LBC6
- Elsewhere: RCSB PDB 4C8D · PDBe 4C8D · UniProt Q7LBC6
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