MolNFT v1 · #177929 · protein
Complex structure of sptf with fe, alpha-ketoglutarate, and andiconin D
7EYS · 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf: “Complex structure of sptf with fe, alpha-ketoglutarate, and andiconin D”. X-ray diffraction, 3 ligands (AKG, 0CC, FE2), 15 pockets (best druggability 0.78). MolNFT v1 #177929 on…
- PDB
- 7EYS
- Type
- protein
- Length
- 1,071 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
- AKG, 0CC, FE2
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf | protein | 277 | 30% helix, 19% strand | A0A6J4CX17 |
| A | 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf | protein | 248 | 31% helix, 21% strand | A0A6J4CX17 |
| B | 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf | protein | 278 | 30% helix, 18% strand | A0A6J4CX17 |
| D | 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf | protein | 268 | 31% helix, 19% strand | A0A6J4CX17 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains C
- 0CC · Andiconin D · ligand · chains C
- FE2 · Fe (II) ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.78 | 0.86 | 49 | AKG, 0CC, FE2 |
| 2 | 393 | 0.66 | 0.79 | 49 | empty |
| 3 | 386 | 0.59 | 0.76 | 36 | empty |
| 4 | 204 | 0.52 | 0.77 | 29 | empty |
| 5 | 230 | 0.52 | 0.76 | 30 | empty |
Interfaces
4 interfaces between chains.
- C–D · 557 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 384 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 161 Ų buried · 2 hydrogen bonds · protein-protein
- C–A · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7EYS · Complex structure of SptF with Fe, alpha-ketoglutarate, and andiconin D · 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 7EYS · PDBe 7EYS · UniProt A0A6J4CX17
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