Research workbench
Pandda analysis group deposition -- crystal structure of JMJD1B in complex with FM001767A
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
- 5RAG
- 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
- O3G, MN, CL
- Pockets
- 11 · 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 | 35% helix, 23% strand | Q7LBC6 |
Ligands and binding sites
- O3G · N-benzyl-1-(4-fluorophenyl)methanamine · ligand · chains A
- 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
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.70 | 0.78 | 79 | MN |
| 2 | 628 | 0.70 | 0.78 | 79 | CL, MN |
| 3 | 113 | 0.50 | 0.81 | 24 | empty |
| 4 | 117 | 0.48 | 0.80 | 20 | empty |
| 5 | 87 | 0.43 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 520 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5RAG · PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM001767a · 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 5RAG · PDBe 5RAG · UniProt Q7LBC6
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