Research workbench
Structure of full length unliganded cody from bacillus subtilis
Analyse Structure of full length unliganded cody from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LNH
- Type
- protein
- Length
- 2,550 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-sensing transcriptional pleiotropic repressor cody
- UniProt
- P39779
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, K | GTP-sensing transcriptional pleiotropic repressor cody | protein | 255 | 53% helix, 19% strand | P39779 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, H, B, G, C, F, D, E, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.86 | 0.90 | 60 | empty |
| 2 | 606 | 0.85 | 0.90 | 70 | empty |
| 3 | 770 | 0.84 | 0.88 | 76 | empty |
| 4 | 762 | 0.84 | 0.88 | 69 | empty |
| 5 | 94 | 0.59 | 0.87 | 20 | empty |
Interfaces
16 interfaces between chains.
- I–K · 1439 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1420 Ų buried · 7 hydrogen bonds · protein-protein
- B–H · 1385 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 1379 Ų buried · 10 hydrogen bonds · protein-protein
- A–G · 1350 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 70 modified (engineered).
Compared structures
- 5LNH · Structure of full length Unliganded CodY from Bacillus subtilis · the same entry in another collection · chain K against K, TM-score 1.00
- P39779 · AlphaFold monomer V2.0 prediction for GTP-sensing transcriptional pleiotropic repressor… · a predicted model of the same protein · chain B against A, TM-score 0.89
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 P39779
- Elsewhere: RCSB PDB 5LNH · PDBe 5LNH · UniProt P39779
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