MolNFT v1 · #177931 · protein
FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase sptf-N65T mutant with andiconin D
7EYU · 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf: “FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase sptf-N65T mutant with andiconin D”. X-ray diffraction, 3 ligands (OGA, 0CC, FE2), 4 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 7EYU
- Type
- protein
- Length
- 535 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf
- UniProt
- A0A6J4CX17
- Ligands
- OGA, 0CC, FE2
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf | protein | 265 | 30% helix, 20% strand | A0A6J4CX17 |
| A | 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf | protein | 270 | 28% helix, 21% strand | A0A6J4CX17 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains B
- 0CC · Andiconin D · ligand · chains B
- FE2 · Fe (II) ion · metal · 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 | 436 | 0.86 | 0.93 | 54 | OGA, 0CC, FE2 |
| 2 | 289 | 0.57 | 0.77 | 32 | FE2 |
| 3 | 74 | 0.48 | 0.83 | 16 | empty |
| 4 | 120 | 0.42 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- B–A · 1767 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 7EYU · Fe(II)/(alpha)ketoglutarate-dependent dioxygenase SptF-N65T mutant with andiconin D · the same entry in another collection · chain B against B, 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 A0A6J4CX17
- Elsewhere: RCSB PDB 7EYU · PDBe 7EYU · UniProt A0A6J4CX17
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