Research workbench
Crystal structure of JMJD5 catalytic core domain in complex with nickle and alpha-kg
Analyse Crystal structure of JMJD5 catalytic core domain in complex with nickle and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UYJ
- 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
- AKG, NI
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 8 (EC 1.14.11.27) | protein | 238 | 26% helix, 32% strand | Q8N371 |
| B | Lysine-specific demethylase 8 (EC 1.14.11.27) | protein | 230 | 27% helix, 35% strand | Q8N371 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.57 | 0.86 | 21 | AKG |
| 2 | 63 | 0.41 | 0.81 | 14 | empty |
| 3 | 51 | 0.35 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 369 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3UYJ · Crystal structure of JMJD5 catalytic core domain in complex with nickle and alpha-KG · 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 0.98
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 Q8N371
- Elsewhere: RCSB PDB 3UYJ · PDBe 3UYJ · UniProt Q8N371
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