Research workbench
FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase sptf apo
Analyse FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase sptf apo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EYR
- Type
- protein
- Length
- 1,099 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
- FE2
- Pockets
- 14 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf | protein | 279 | 31% helix, 16% strand | A0A6J4CX17 |
| A | 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf | protein | 279 | 30% helix, 17% strand | A0A6J4CX17 |
| B | 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf | protein | 279 | 30% helix, 19% strand | A0A6J4CX17 |
| D | 2-OXOGLUTARATE/FE(II)-dependent dioxygenase sptf | protein | 262 | 31% helix, 20% strand | A0A6J4CX17 |
Ligands and binding sites
- 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
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.66 | 0.80 | 38 | empty |
| 2 | 282 | 0.63 | 0.81 | 35 | empty |
| 3 | 192 | 0.53 | 0.78 | 28 | FE2 |
| 4 | 179 | 0.52 | 0.79 | 31 | FE2 |
| 5 | 178 | 0.51 | 0.78 | 30 | FE2 |
Interfaces
5 interfaces between chains.
- C–A · 673 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 414 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 398 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 143 Ų buried · 3 hydrogen bonds · protein-protein
- C–B · 32 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7EYR · Fe(II)/(alpha)ketoglutarate-dependent dioxygenase SptF apo · 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 7EYR · PDBe 7EYR · UniProt A0A6J4CX17
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