MolNFT v1 · #132800 · protein
Pandda analysis group deposition -- crystal structure of JMJD1B in complex with FM010010A
5RB5 · Lysine-specific demethylase 3B: “Pandda analysis group deposition -- crystal structure of JMJD1B in complex with FM010010A”. X-ray diffraction, 3 ligands (S9S, MN, CL), 12 pockets (best druggability 0.69). MolNFT v1 #132800 on…
- PDB
- 5RB5
- 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
- S9S, MN, CL
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 3B (EC 1.14.11.-) | protein | 340 | 32% helix, 24% strand | Q7LBC6 |
| B | Lysine-specific demethylase 3B (EC 1.14.11.-) | protein | 344 | 34% helix, 23% strand | Q7LBC6 |
Ligands and binding sites
- S9S · ~{N}-[2-(4-fluorophenyl)ethyl]methanesulfonamide · 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 | 646 | 0.69 | 0.77 | 74 | empty |
| 2 | 520 | 0.68 | 0.79 | 63 | MN |
| 3 | 103 | 0.51 | 0.82 | 23 | empty |
| 4 | 164 | 0.49 | 0.77 | 25 | S9S |
| 5 | 71 | 0.44 | 0.81 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 523 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5RB5 · PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM010010a · 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 5RB5 · PDBe 5RB5 · UniProt Q7LBC6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.