MolNFT v1 · #119502 · protein
Crystal structure of the catalytic domain of human JARID1B in complex with succinate
5FY4 · Lysine-specific demethylase 5B: “Crystal structure of the catalytic domain of human JARID1B in complex with succinate”. X-ray diffraction, 3 ligands (FUM, MN, ZN), 5 pockets (best druggability 0.74). MolNFT v1 #119502 on GenesisL1…
- PDB
- 5FY4
- Type
- protein
- Length
- 454 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 5B
- EC
- 1.14.11.-
- UniProt
- Q9UGL1
- Ligands
- FUM, MN, ZN
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5B (EC 1.14.11.-) | protein | 454 | 38% helix, 20% strand | Q9UGL1 |
Ligands and binding sites
- FUM · Fumaric acid · ligand · chains A
- MN · Manganese (II) ion · metal · 5 copies · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.74 | 0.87 | 32 | MN |
| 2 | 187 | 0.74 | 0.90 | 24 | EDO |
| 3 | 315 | 0.71 | 0.84 | 50 | MN, FUM |
| 4 | 96 | 0.37 | 0.75 | 19 | empty |
| 5 | 58 | 0.32 | 0.76 | 15 | EDO |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5FY4 · Crystal structure of the catalytic domain of human JARID1B in complex with succinate · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UGL1 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 5B (Q9UGL1) · a predicted model of the same protein · chain A 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 Q9UGL1
- Elsewhere: RCSB PDB 5FY4 · PDBe 5FY4 · UniProt Q9UGL1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.