MolNFT v1 · #125951 · protein
Structure of full length cody from bacillus subtilis in complex with ile
5LOE · GTP-sensing transcriptional pleiotropic repressor cody: “Structure of full length cody from bacillus subtilis in complex with ile”. X-ray diffraction, 1 ligand (ILE), 16 pockets (best druggability 0.84). MolNFT v1 #125951 on…
- 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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