Research workbench
Crystal structure of KDM5B in complex with KDOPZ29A
Analyse Crystal structure of KDM5B in complex with KDOPZ29A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EIU
- Type
- protein
- Length
- 454 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 5B,LYSINE-specific demethylase 5B
- EC
- 1.14.11.-
- UniProt
- Q9UGL1
- Ligands
- B6T, ZN, MN
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5B,LYSINE-specific demethylase 5B (EC 1.14.11.-) | protein | 454 | 38% helix, 20% strand | Q9UGL1 |
Ligands and binding sites
- B6T · 8-oxidanyl-6-phenyl-7-propan-2-yl-imidazo[1,2-b]pyridazine-3-carbonitrile · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 7 copies · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.82 | 0.85 | 67 | B6T, DMS |
| 2 | 210 | 0.75 | 0.90 | 25 | EDO |
| 3 | 123 | 0.47 | 0.78 | 21 | empty |
| 4 | 58 | 0.40 | 0.81 | 21 | DMS |
| 5 | 72 | 0.33 | 0.75 | 17 | empty |
Compared structures
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 Q9UGL1
- Elsewhere: RCSB PDB 6EIU · PDBe 6EIU · UniProt Q9UGL1
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