Research workbench
Crystal structure of KDM3B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol
Analyse Crystal structure of KDM3B 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
- 6RBJ
- Type
- protein
- Length
- 676 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.093
- Source
- Homo sapiens
- Molecule
- Lysine-specific demethylase 3B
- EC
- 1.14.11.-
- UniProt
- Q7LBC6
- Ligands
- JX8, MN, CL
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.093 · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 3B (EC 1.14.11.-) | protein | 335 | 35% helix, 24% strand | Q7LBC6 |
| B | Lysine-specific demethylase 3B (EC 1.14.11.-) | protein | 341 | 35% helix, 23% strand | Q7LBC6 |
Ligands and binding sites
- JX8 · 5-(1~{H}-1,2,3,4-tetrazol-5-yl)quinolin-8-ol · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.69 | 0.78 | 73 | EDO, JX8, MN |
| 2 | 513 | 0.68 | 0.79 | 64 | EDO, JX8, MN |
| 3 | 95 | 0.49 | 0.82 | 24 | empty |
| 4 | 103 | 0.45 | 0.79 | 21 | empty |
| 5 | 89 | 0.45 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 537 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6RBJ · Crystal structure of KDM3B 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
- Q7LBC6 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 3B (Q7LBC6) · a predicted model of the same protein · chain B 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 Q7LBC6
- Elsewhere: RCSB PDB 6RBJ · PDBe 6RBJ · UniProt Q7LBC6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.