MolNFT v1 · #177812 · protein
Crystal structures of 2-oxoglutarate dependent dioxygenase (CTB9) in complex with N-oxalylglycine
7EUT · 2-oxoglutarate (2-og)-dependent dioxygenase: “Crystal structures of 2-oxoglutarate dependent dioxygenase (CTB9) in complex with N-oxalylglycine”. X-ray diffraction, 2 ligands (OGA, CU), 7 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 7EUT
- Type
- protein
- Length
- 576 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-oxoglutarate (2-og)-dependent dioxygenase
- Ligands
- OGA, CU
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-oxoglutarate (2-og)-dependent dioxygenase | protein | 289 | 20% helix, 33% strand | — |
| B | 2-oxoglutarate (2-og)-dependent dioxygenase | protein | 287 | 22% helix, 33% strand | — |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, B
- CU · Copper (II) ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.73 | 0.84 | 49 | OGA, EDO |
| 2 | 419 | 0.69 | 0.81 | 48 | empty |
| 3 | 140 | 0.52 | 0.80 | 26 | empty |
| 4 | 133 | 0.48 | 0.78 | 22 | GOL |
| 5 | 134 | 0.44 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1216 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7EUT · Crystal structures of 2-oxoglutarate dependent dioxygenase (CTB9) in complex with… · 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
- Elsewhere: RCSB PDB 7EUT · PDBe 7EUT
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