MolNFT v1 · #122636 · protein
A high resolution structure of a linked KDM5A jmj domain with alpha- ketoglutarate
5IVB · Lysine-specific demethylase 5A,LYSINE-specific demethylase…: “A high resolution structure of a linked KDM5A jmj domain with alpha- ketoglutarate”. X-ray diffraction, 2 ligands (AKG, MN), 2 pockets (best druggability 0.69). MolNFT v1…
- PDB
- 5IVB
- Type
- protein
- Length
- 293 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 5A,LYSINE-specific demethylase 5A
- EC
- 1.14.11.-
- UniProt
- P29375
- Ligands
- AKG, MN
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5A,LYSINE-specific demethylase 5A (EC 1.14.11.-) | protein | 293 | 32% helix, 25% strand | P29375 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.69 | 0.79 | 68 | AKG, MN, GOL |
| 2 | 51 | 0.40 | 0.82 | 15 | empty |
Compared structures
- 5IVB · A High Resolution Structure of a Linked KDM5A Jmj Domain with Alpha-Ketoglutarate · the same entry in another collection · chain A against A, TM-score 1.00
- P29375 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 5A (P29375) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P29375
- Elsewhere: RCSB PDB 5IVB · PDBe 5IVB · UniProt P29375
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