Research workbench
Crystal structure of the epimerase snon in complex with FE3+, alpha ketoglutarate and nogalamycin ro
Analyse Crystal structure of the epimerase snon in complex with FE3+, alpha… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EQU
- Type
- protein
- Length
- 1,024 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SNON,SNON
- UniProt
- Q9RN67, Q9EYI0
- Ligands
- AKG, 5R6, FE
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | SNON,SNON | protein | 256 | 29% helix, 27% strand | Q9RN67, Q9EYI0 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, C, D
- 5R6 · Nogalamycin RO · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.82 | 0.84 | 94 | empty |
| 2 | 296 | 0.76 | 0.87 | 34 | FE, AKG, 5R6 |
| 3 | 305 | 0.75 | 0.87 | 36 | FE, AKG, 5R6 |
| 4 | 1081 | 0.74 | 0.77 | 80 | empty |
| 5 | 286 | 0.74 | 0.86 | 41 | AKG, 5R6 |
Interfaces
5 interfaces between chains.
- A–D · 684 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 625 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 603 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 143 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 99 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5EQU · Crystal structure of the epimerase SnoN in complex with Fe3+, alpha ketoglutarate and… · 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 5EQU · PDBe 5EQU · UniProt Q9RN67 · UniProt Q9EYI0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.