Research workbench
Crystal structure of the catalytic domain of human JARID1B in complex with MC1648
Analyse Crystal structure of the catalytic domain of human JARID1B in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FYB
- Type
- protein
- Length
- 455 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 5B, lysine-specific demethylase 5B
- EC
- 1.14.11.-
- UniProt
- Q9UGL1
- Ligands
- 77J, MN, ZN
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5B, lysine-specific demethylase 5B (EC 1.14.11.-) | protein | 455 | 37% helix, 21% strand | Q9UGL1 |
Ligands and binding sites
- 77J · N-hydroxy-3-[(6-oxo-4-phenyl-1,6-dihydropyrimidin-2-yl)sulfanyl]propanamide · ligand · 2 copies · chains A
- MN · Manganese (II) ion · metal · 4 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 16 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 4 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 | 479 | 0.78 | 0.85 | 51 | MN, 77J, EDO, DMS |
| 2 | 187 | 0.74 | 0.90 | 24 | EDO |
| 3 | 280 | 0.73 | 0.86 | 32 | DMS |
| 4 | 140 | 0.46 | 0.77 | 25 | empty |
| 5 | 59 | 0.33 | 0.76 | 15 | EDO |
Compared structures
- 5FYB · Crystal structure of the catalytic domain of human JARID1B in complex with MC1648 · 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 0.96
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 Q9UGL1
- Elsewhere: RCSB PDB 5FYB · PDBe 5FYB · UniProt Q9UGL1
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