Research workbench
CEKDM7A from C.ELEGANS, complex with alpha-kg
Analyse CEKDM7A from C.ELEGANS, complex with alpha-kg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PUQ
- Type
- protein
- Length
- 943 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 7 homolog
- EC
- 1.14.11.27
- UniProt
- Q9GYI0
- Ligands
- AKG, ZN, FE2
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 7 homolog (EC 1.14.11.27) | protein | 472 | 38% helix, 21% strand | Q9GYI0 |
| C | Lysine-specific demethylase 7 homolog (EC 1.14.11.27) | protein | 471 | 38% helix, 21% strand | Q9GYI0 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, C
- ZN · Zinc ion · metal · 4 copies · chains A, C
- FE2 · Fe (II) ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.77 | 0.81 | 63 | AKG, GOL |
| 2 | 1190 | 0.77 | 0.79 | 112 | empty |
| 3 | 823 | 0.75 | 0.79 | 57 | FE2, AKG, GOL |
| 4 | 161 | 0.60 | 0.83 | 24 | empty |
| 5 | 181 | 0.60 | 0.83 | 22 | empty |
Interfaces
1 interface between chains.
- A–C · 518 Ų buried · 8 hydrogen bonds · protein-protein
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 Q9GYI0
- Elsewhere: RCSB PDB 3PUQ · PDBe 3PUQ · UniProt Q9GYI0
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