MolNFT v1 · #132793 · protein
Pandda analysis group deposition -- crystal structure of JMJD1B in complex with FM001469A
5RAY · Lysine-specific demethylase 3B: “Pandda analysis group deposition -- crystal structure of JMJD1B in complex with FM001469A”. X-ray diffraction, 3 ligands (S9M, MN, CL), 10 pockets (best druggability 0.70). MolNFT v1 #132793 on…
- PDB
- 5RAY
- 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
- S9M, MN, CL
- Pockets
- 10 · best druggability 0.70
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 | 33% helix, 24% strand | Q7LBC6 |
| B | Lysine-specific demethylase 3B (EC 1.14.11.-) | protein | 344 | 33% helix, 23% strand | Q7LBC6 |
Ligands and binding sites
- S9M · 2,4-difluoro-6-[(3S)-pyrazolidin-3-yl]phenol · 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
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 631 | 0.70 | 0.78 | 72 | MN |
| 2 | 633 | 0.69 | 0.78 | 83 | CL, MN |
| 3 | 104 | 0.49 | 0.80 | 23 | empty |
| 4 | 113 | 0.47 | 0.79 | 19 | empty |
| 5 | 82 | 0.43 | 0.79 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 511 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5RAY · PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM001469a · 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 5RAY · PDBe 5RAY · UniProt Q7LBC6
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