Research workbench
Pandda analysis group deposition -- crystal structure of JMJD1B in complex with XS039249D
Analyse Pandda analysis group deposition -- crystal structure of JMJD1B in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5RB3
- Type
- protein
- Length
- 684 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 3B
- EC
- 1.14.11.-
- UniProt
- Q7LBC6
- Ligands
- MPV, MN, CL
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 3B (EC 1.14.11.-) | protein | 340 | 33% helix, 24% strand | Q7LBC6 |
| B | Lysine-specific demethylase 3B (EC 1.14.11.-) | protein | 344 | 34% helix, 23% strand | Q7LBC6 |
Ligands and binding sites
- MPV · 1-methyl-3-(thiophen-2-yl)-1H-pyrazol-5-amine · ligand · 3 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.70 | 0.78 | 69 | MN |
| 2 | 617 | 0.69 | 0.78 | 79 | CL, MN |
| 3 | 62 | 0.59 | 0.90 | 19 | empty |
| 4 | 115 | 0.46 | 0.79 | 19 | empty |
| 5 | 50 | 0.42 | 0.83 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 505 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5RB3 · PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with XS039249d · the same entry in another collection · chain A against A, TM-score 1.00
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 5RB3 · PDBe 5RB3 · UniProt Q7LBC6
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