Research workbench
Crystal structure of the bacillus subtilis ykui protein, with an eal domain, in complex with substrate C-di-gmp and calcium
Analyse Crystal structure of the bacillus subtilis ykui protein, with an eal domain, in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W27
- Type
- protein
- Length
- 796 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- BACILLUS SUBTILIS
- Molecule
- Ykui protein
- UniProt
- O35014
- Ligands
- 5GP, CA
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · resolution 2.8 · 2 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ykui protein | protein | 401 | 43% helix, 24% strand | O35014 |
| B | Ykui protein | protein | 395 | 43% helix, 23% strand | O35014 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.87 | 0.88 | 98 | empty |
| 2 | 538 | 0.69 | 0.79 | 51 | 5GP, CA |
| 3 | 71 | 0.68 | 0.94 | 16 | empty |
| 4 | 427 | 0.66 | 0.79 | 47 | 5GP, CA |
| 5 | 307 | 0.63 | 0.80 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 3249 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 2W27 · Crystal structure of the bacillus subtilis ykui protein, with an eal domain, in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- O35014 · AlphaFold monomer V2.0 prediction for uncharacterized eal-domain containing protein ykui… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O35014
- Elsewhere: RCSB PDB 2W27 · PDBe 2W27 · UniProt O35014
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