MolNFT v1 · #113052 · protein
Crystal structure of human plu-1 (JARID1B) in complex with KDM5-C49 (2-(((2-((2-(DIMETHYLAMINO)ETHYL)(ETHYL)AMINO)-2- OXOETHYL)AMINO)METHYL) isonicotinic acid).
5A3T · Lysine-specific demethylase 5B: “Crystal structure of human plu-1 (JARID1B) in complex with KDM5-C49…”. X-ray diffraction, 4 ligands (MMK, ZN, NI), 6 pockets (best druggability 0.77). MolNFT v1 #113052 on GenesisL1: 3D structure…
- PDB
- 5A3T
- 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
- MMK, ZN, NI, MN
- Pockets
- 6 · best druggability 0.77
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
- MMK · 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid · ligand · chains A
- ZN · Zinc ion · metal · chains A
- NI · Nickel (II) ion · metal · chains A
- MN · Manganese (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 7 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.77 | 0.87 | 41 | MMK, MN |
| 2 | 293 | 0.75 | 0.88 | 35 | EPE |
| 3 | 193 | 0.73 | 0.90 | 24 | EDO |
| 4 | 105 | 0.47 | 0.80 | 22 | empty |
| 5 | 71 | 0.33 | 0.75 | 17 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5A3T · Crystal structure of human PLU-1 (JARID1B) in complex with KDM5-C49… · 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 5A3T · PDBe 5A3T · UniProt Q9UGL1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.