Research workbench
N-terminal gaf domain of transcriptional pleiotropic repressor cody
Analyse N-terminal gaf domain of transcriptional pleiotropic repressor cody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GX5
- Type
- protein
- Length
- 636 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
- PCG, SO4
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-sensing transcriptional pleiotropic repressor cody | protein | 157 | 47% helix, 23% strand | P39779 |
| B | GTP-sensing transcriptional pleiotropic repressor cody | protein | 160 | 46% helix, 23% strand | P39779 |
| C | GTP-sensing transcriptional pleiotropic repressor cody | protein | 161 | 47% helix, 22% strand | P39779 |
| D | GTP-sensing transcriptional pleiotropic repressor cody | protein | 158 | 46% helix, 23% strand | P39779 |
Ligands and binding sites
- PCG · Cyclic guanosine monophosphate · ligand · chains C
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 11 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains C
- P6G · Hexaethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.63 | 0.75 | 35 | SO4, GOL |
| 2 | 336 | 0.59 | 0.77 | 40 | GOL, SO4 |
| 3 | 335 | 0.59 | 0.77 | 41 | GOL |
| 4 | 62 | 0.55 | 0.88 | 18 | GOL |
| 5 | 56 | 0.51 | 0.86 | 16 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 1101 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1086 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 247 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2GX5 · N-terminal GAF domain of transcriptional pleiotropic repressor CodY · 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 0.86
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 2GX5 · PDBe 2GX5 · UniProt P39779
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