MolNFT v1 · #62474 · protein
Crystal structure of degv family protein CG2579 from corynebacterium glutamicum
3EGL: “Crystal structure of degv family protein CG2579 from corynebacterium glutamicum”. X-ray diffraction, 1 ligand (PLM), 12 pockets (best druggability 0.80). MolNFT v1 #62474 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3EGL
- Type
- protein
- Length
- 793 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Degv family protein
- UniProt
- Q8NN60
- Ligands
- PLM
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Degv family protein | protein | 264 | 40% helix, 23% strand | Q8NN60 |
| B | Degv family protein | protein | 266 | 41% helix, 24% strand | Q8NN60 |
| C | Degv family protein | protein | 263 | 40% helix, 22% strand | Q8NN60 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.80 | 0.95 | 33 | PLM |
| 2 | 143 | 0.79 | 0.96 | 35 | PLM |
| 3 | 151 | 0.79 | 0.95 | 30 | PLM |
| 4 | 517 | 0.67 | 0.78 | 66 | empty |
| 5 | 389 | 0.63 | 0.78 | 42 | empty |
Interfaces
3 interfaces between chains.
- A–B · 545 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 388 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 173 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 51 modified (engineered, methylation).
Compared structures
- 3EGL · Crystal Structure of DegV Family Protein Cg2579 from Corynebacterium glutamicum · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NN60 · AlphaFold monomer V2.0 prediction for degv domain-containing protein CGL2349/CG2579… · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q8NN60
- Elsewhere: RCSB PDB 3EGL · PDBe 3EGL · UniProt Q8NN60
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