Research workbench
Crystal structures of 2-oxoglutarate dependent dioxygenase (CTB9) in complex with N-oxalylglycine and pre-cercosporin
Analyse Crystal structures of 2-oxoglutarate dependent dioxygenase (CTB9) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EUU
- 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, JD9, CU
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-oxoglutarate (2-og)-dependent dioxygenase | protein | 288 | 21% helix, 33% strand | — |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, B
- JD9 · 2,6,11-trimethoxy-4,7,9-tris(oxidanyl)-1,12-bis[(2R)-2-oxidanylpropyl]perylene-3,10-dione · ligand · 2 copies · chains A, B
- CU · Copper (II) ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.74 | 0.82 | 68 | CU, OGA, JD9 |
| 2 | 532 | 0.72 | 0.81 | 70 | JD9, EDO |
| 3 | 129 | 0.48 | 0.79 | 21 | empty |
| 4 | 53 | 0.37 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1245 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7EUU · 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 7EUU · PDBe 7EUU
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