Research workbench
Crystal structure of the catalytic domain of human JARID1B in complex with D-2-hydroxyglutarate
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
- 5FYS
- Type
- protein
- Length
- 453 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
- 2HG, ZN, MN, CL
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5B (EC 1.14.11.-) | protein | 453 | 39% helix, 20% strand | Q9UGL1 |
Ligands and binding sites
- 2HG · (2R)-2-hydroxypentanedioic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 14 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 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 | 396 | 0.78 | 0.87 | 47 | MN, EDO, 2HG |
| 2 | 261 | 0.74 | 0.87 | 30 | EPE |
| 3 | 187 | 0.74 | 0.90 | 23 | EDO |
| 4 | 132 | 0.45 | 0.77 | 22 | empty |
| 5 | 73 | 0.33 | 0.75 | 18 | EDO |
Compared structures
- 5FYS · Crystal structure of the catalytic domain of human JARID1B in complex with… · 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 5FYS · PDBe 5FYS · UniProt Q9UGL1
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