Research workbench
Crystal structure of cody from staphylococcus aureus with GTP and ile
Analyse Crystal structure of cody from staphylococcus aureus with GTP and ile in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EY1
- Type
- protein
- Length
- 408 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-sensing transcriptional pleiotropic repressor cody
- UniProt
- A7X1N2
- Ligands
- ILE, GTP
- Pockets
- 8 · best druggability 0.50
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 | 240 | 51% helix, 18% strand | A7X1N2 |
| B | GTP-sensing transcriptional pleiotropic repressor cody | protein | 168 | 47% helix, 21% strand | A7X1N2 |
Ligands and binding sites
- ILE · Isoleucine · ligand · 2 copies · chains A, B
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.50 | 0.83 | 18 | ILE |
| 2 | 67 | 0.45 | 0.82 | 16 | ILE |
| 3 | 87 | 0.41 | 0.78 | 13 | empty |
| 4 | 82 | 0.40 | 0.78 | 14 | empty |
| 5 | 71 | 0.39 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1370 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5EY1 · Crystal structure of CodY from Staphylococcus aureus with GTP and Ile · the same entry in another collection · chain A against A, TM-score 1.00
- A7X1N2 · AlphaFold monomer V2.0 prediction for GTP-sensing transcriptional pleiotropic repressor… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 A7X1N2
- Elsewhere: RCSB PDB 5EY1 · PDBe 5EY1 · UniProt A7X1N2
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