Research workbench
The structure of the cofactor binding gaf domain of the nutrient sensor cody from clostridium difficile
Analyse The structure of the cofactor binding gaf domain of the nutrient sensor cody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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