MolNFT v1 · #127572 · protein
The structure of the cofactor binding gaf domain of the nutrient sensor cody from clostridium difficile
5N0L · GTP-sensing transcriptional pleiotropic repressor cody: “The structure of the cofactor binding gaf domain of the nutrient sensor cody from clostridium difficile”. X-ray diffraction, 1 ligand (ILE), 14 pockets (best druggability…
- PDB
- 5N0L
- Type
- protein
- Length
- 936 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-sensing transcriptional pleiotropic repressor cody
- UniProt
- A0A031WD25
- Ligands
- ILE
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | GTP-sensing transcriptional pleiotropic repressor cody | protein | 156 | 40% helix, 27% strand | A0A031WD25 |
Ligands and binding sites
- ILE · Isoleucine · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.73 | 0.99 | 14 | ILE |
| 2 | 51 | 0.72 | 0.98 | 14 | ILE |
| 3 | 748 | 0.70 | 0.77 | 72 | empty |
| 4 | 493 | 0.70 | 0.80 | 51 | empty |
| 5 | 422 | 0.67 | 0.80 | 50 | empty |
Interfaces
15 interfaces between chains.
- B–C · 1466 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 1448 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1414 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 515 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 511 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5N0L · The structure of the cofactor binding GAF domain of the nutrient sensor CodY from… · the same entry in another collection · chain E against E, 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 A0A031WD25
- Elsewhere: RCSB PDB 5N0L · PDBe 5N0L · UniProt A0A031WD25
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