Research workbench
Crystal structure of human plu-1 (JARID1B) in complex with KDOAM25A
Analyse Crystal structure of human plu-1 (JARID1B) in complex with KDOAM25A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A3N
- Type
- protein
- Length
- 456 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
- LQT, MN, ZN, PO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5B (EC 1.14.11.-) | protein | 456 | 37% helix, 19% strand | Q9UGL1 |
Ligands and binding sites
- LQT · 2-[[[2-[2-(dimethylamino)ethyl-ethyl-amino]-2-oxidanylidene-ethyl]amino]methyl]pyridine-4-carboxamide · ligand · chains A
- MN · Manganese (II) ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.76 | 0.88 | 32 | EPE |
| 2 | 190 | 0.74 | 0.90 | 26 | empty |
| 3 | 447 | 0.73 | 0.83 | 50 | MN, LQT, DMS |
| 4 | 176 | 0.47 | 0.75 | 28 | EDO |
| 5 | 81 | 0.43 | 0.80 | 21 | empty |
Compared structures
- 5A3N · Crystal structure of human PLU-1 (JARID1B) in complex with KDOAM25a · 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 5A3N · PDBe 5A3N · UniProt Q9UGL1
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