Research workbench
Pandda analysis group deposition -- crystal structure of JMJD1B in complex with FM010013A
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
- 5RAZ
- 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
- K0G, MN, CL
- Pockets
- 9 · 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 | 34% helix, 24% strand | Q7LBC6 |
| B | Lysine-specific demethylase 3B (EC 1.14.11.-) | protein | 344 | 34% helix, 23% strand | Q7LBC6 |
Ligands and binding sites
- K0G · N-phenyl-N'-pyridin-3-ylurea · 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 633 | 0.70 | 0.78 | 81 | CL, MN |
| 2 | 624 | 0.70 | 0.78 | 72 | MN |
| 3 | 200 | 0.60 | 0.82 | 31 | K0G |
| 4 | 115 | 0.49 | 0.80 | 21 | empty |
| 5 | 101 | 0.43 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 520 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5RAZ · PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM010013a · 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 5RAZ · PDBe 5RAZ · UniProt Q7LBC6
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