MolNFT v1 · #177930 · protein
FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase sptf with andilesin C and nog
7EYT · 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf: “FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase sptf with andilesin C and nog”. X-ray diffraction, 3 ligands (OGA, 0I3, FE2), 12 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 7EYT
- Type
- protein
- Length
- 1,078 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf
- UniProt
- A0A6J4CX17
- Ligands
- OGA, 0I3, FE2
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf | protein | 277 | 31% helix, 21% strand | A0A6J4CX17 |
| A | 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf | protein | 258 | 31% helix, 21% strand | A0A6J4CX17 |
| B | 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf | protein | 267 | 31% helix, 19% strand | A0A6J4CX17 |
| D | 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf | protein | 276 | 30% helix, 18% strand | A0A6J4CX17 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains C
- 0I3 · Andilesin C · ligand · chains C
- FE2 · Fe (II) ion · metal · 4 copies · chains C, A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.87 | 0.94 | 54 | OGA, 0I3, FE2 |
| 2 | 377 | 0.68 | 0.81 | 42 | FE2 |
| 3 | 569 | 0.65 | 0.76 | 67 | FE2 |
| 4 | 343 | 0.59 | 0.77 | 35 | FE2 |
| 5 | 190 | 0.52 | 0.78 | 24 | empty |
Interfaces
3 interfaces between chains.
- C–B · 1949 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 1700 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 454 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7EYT · Fe(II)/(alpha)ketoglutarate-dependent dioxygenase SptF with andilesin C and NOG · the same entry in another collection · chain C against C, 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 7EYT · PDBe 7EYT · UniProt A0A6J4CX17
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