Research workbench
Structure of full length cody from bacillus subtilis in complex with ile
Analyse Structure of full length cody from bacillus subtilis in complex with ile in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LOE
- Type
- protein
- Length
- 1,029 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-sensing transcriptional pleiotropic repressor cody
- UniProt
- P39779
- Ligands
- ILE
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-sensing transcriptional pleiotropic repressor cody | protein | 258 | 50% helix, 19% strand | P39779 |
| B, C, D | GTP-sensing transcriptional pleiotropic repressor cody | protein | 257 | 51% helix, 19% strand | P39779 |
Ligands and binding sites
- ILE · Isoleucine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.84 | 0.84 | 128 | empty |
| 2 | 437 | 0.75 | 0.85 | 59 | empty |
| 3 | 166 | 0.66 | 0.86 | 25 | empty |
| 4 | 168 | 0.66 | 0.86 | 25 | empty |
| 5 | 70 | 0.50 | 0.84 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1657 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1468 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 880 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 857 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 137 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5LOE · Structure of full length Cody from Bacillus subtilis in complex with Ile · the same entry in another collection · chain D against D, TM-score 1.00
- P39779 · AlphaFold monomer V2.0 prediction for GTP-sensing transcriptional pleiotropic repressor… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 5LOE · PDBe 5LOE · UniProt P39779
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