MolNFT v1 · #119506 · protein
Crystal structure of the catalytic domain of human JARID1B in complex with pyruvate
5FY9 · Lysine-specific demethylase 5B, lysine-specific demethylase…: “Crystal structure of the catalytic domain of human JARID1B in complex with pyruvate”. X-ray diffraction, 3 ligands (PYR, MN, ZN), 5 pockets (best druggability 0.78).…
- PDB
- 5FY9
- Type
- protein
- Length
- 460 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
- PYR, MN, ZN
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5B, lysine-specific demethylase 5B (EC 1.14.11.-) | protein | 460 | 38% helix, 20% strand | Q9UGL1 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · chains A
- MN · Manganese (II) ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 9 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 | 429 | 0.78 | 0.86 | 52 | MN, EDO, PYR |
| 2 | 189 | 0.75 | 0.91 | 23 | empty |
| 3 | 280 | 0.74 | 0.87 | 30 | EPE |
| 4 | 116 | 0.42 | 0.76 | 21 | empty |
| 5 | 65 | 0.34 | 0.77 | 17 | EDO |
Compared structures
- 5FY9 · Crystal structure of the catalytic domain of human JARID1B in complex with pyruvate · 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 0.95
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 5FY9 · PDBe 5FY9 · UniProt Q9UGL1
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