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Crystal structure of non-heme alpha ketoglutarate dependent carbocyclase snok from nogalamycin biosynthesis
Analyse Crystal structure of non-heme alpha ketoglutarate dependent carbocyclase snok… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EPA
- Type
- protein
- Length
- 1,543 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Snok
- UniProt
- Q9RN60
- Ligands
- AKG, FE, MG
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Snok | protein | 258 | 28% helix, 27% strand | Q9RN60 |
| F | Snok | protein | 253 | 27% helix, 28% strand | Q9RN60 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 6 copies · chains A, B, C, D, E, F
- FE · Fe (III) ion · metal · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 3 copies · chains 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.85 | 0.86 | 120 | AKG, FE |
| 2 | 503 | 0.79 | 0.86 | 56 | FE, AKG |
| 3 | 765 | 0.79 | 0.82 | 76 | AKG |
| 4 | 539 | 0.78 | 0.85 | 52 | AKG |
| 5 | 976 | 0.77 | 0.79 | 76 | empty |
Interfaces
9 interfaces between chains.
- A–E · 775 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 638 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 625 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 416 Ų buried · 2 hydrogen bonds · protein-protein
- C–F · 299 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5EPA · Crystal structure of non-heme alpha ketoglutarate dependent carbocyclase SnoK from… · 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
- Every structure of UniProt Q9RN60
- Elsewhere: RCSB PDB 5EPA · PDBe 5EPA · UniProt Q9RN60
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