Research workbench
Crystal structure of KDM5B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol
Analyse Crystal structure of KDM5B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RBI
- Type
- protein
- Length
- 454 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.21
- Source
- Homo sapiens
- Molecule
- Lysine-specific demethylase 5B,Lysine-specific demethylase 5B
- EC
- 1.14.11.-
- UniProt
- Q9UGL1
- Ligands
- JX8, ZN, NA, MN, PO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.21 · 1 distinct chain · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5B,Lysine-specific demethylase 5B (EC 1.14.11.-) | protein | 454 | 37% helix, 21% strand | Q9UGL1 |
Ligands and binding sites
- JX8 · 5-(1~{H}-1,2,3,4-tetrazol-5-yl)quinolin-8-ol · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- MN · Manganese (II) ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · 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 | 424 | 0.78 | 0.86 | 43 | MN, JX8, EDO |
| 2 | 301 | 0.75 | 0.87 | 31 | NA |
| 3 | 207 | 0.73 | 0.89 | 23 | empty |
| 4 | 119 | 0.40 | 0.74 | 23 | empty |
| 5 | 52 | 0.35 | 0.79 | 14 | empty |
Compared structures
- 6RBI · Crystal structure of KDM5B in complex with 5-(1H-tetrazol-5-yl) quinolin-8-ol · 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 6RBI · PDBe 6RBI · UniProt Q9UGL1
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