Research workbench
Crystal structure of JMJD5 domain of human lysine-specific demethylase 8 (KDM8) in complex with N-oxalylglycine (nog)
Analyse Crystal structure of JMJD5 domain of human lysine-specific demethylase 8 (KDM8)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AAP
- Type
- protein
- Length
- 468 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 8
- EC
- 1.14.11.27
- UniProt
- Q8N371
- Ligands
- OGA, ZN
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 8 (EC 1.14.11.27) | protein | 235 | 24% helix, 35% strand | Q8N371 |
| B | Lysine-specific demethylase 8 (EC 1.14.11.27) | protein | 233 | 24% helix, 35% strand | Q8N371 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.61 | 0.82 | 30 | OGA |
| 2 | 166 | 0.49 | 0.77 | 24 | empty |
| 3 | 169 | 0.40 | 0.72 | 23 | empty |
| 4 | 53 | 0.33 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 33 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4AAP · Crystal structure of JMJD5 domain of human Lysine-specific demethylase 8 (KDM8) in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N371 · AlphaFold monomer V2.0 prediction for bifunctional peptidase and arginyl-hydroxylase… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q8N371
- Elsewhere: RCSB PDB 4AAP · PDBe 4AAP · UniProt Q8N371
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