MolNFT v1 · #118012 · protein
Crystal structure of the non-heme alpha ketoglutarate dependent epimerase snon from nogalamycin biosynthesis
5EP9 · SNON,EPIMERASE snon: “Crystal structure of the non-heme alpha ketoglutarate dependent epimerase snon from nogalamycin biosynthesis”. X-ray diffraction, 2 ligands (AKG, FE), 11 pockets (best druggability 0.87). MolNFT v1 #118012 on…
- PDB
- 5EP9
- Type
- protein
- Length
- 994 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SNON,EPIMERASE snon
- UniProt
- Q9RN67, Q9EYI0
- Ligands
- AKG, FE
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SNON,EPIMERASE snon | protein | 257 | 28% helix, 27% strand | Q9RN67, Q9EYI0 |
| B | SNON,EPIMERASE snon | protein | 254 | 28% helix, 28% strand | Q9RN67, Q9EYI0 |
| C | SNON,EPIMERASE snon | protein | 241 | 30% helix, 30% strand | Q9RN67, Q9EYI0 |
| D | SNON,EPIMERASE snon | protein | 242 | 30% helix, 29% strand | Q9RN67, Q9EYI0 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.87 | 0.88 | 102 | AKG, FE |
| 2 | 567 | 0.82 | 0.88 | 69 | empty |
| 3 | 407 | 0.73 | 0.83 | 44 | AKG, FE |
| 4 | 977 | 0.71 | 0.75 | 76 | ACT |
| 5 | 349 | 0.71 | 0.83 | 37 | AKG, FE |
Interfaces
5 interfaces between chains.
- C–D · 854 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 818 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 607 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 163 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 45 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5EP9 · Crystal structure of the non-heme alpha ketoglutarate dependent epimerase SnoN 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 Q9RN67
- Every structure of UniProt Q9EYI0
- Elsewhere: RCSB PDB 5EP9 · PDBe 5EP9 · UniProt Q9RN67 · UniProt Q9EYI0
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