Research workbench
Crystal structure of the catalytic domain of human JARID1B in complex with succinate
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
- 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
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