Research workbench
Crystal structure of the bacillus subtilis ykui protein, with an eal domain.
Analyse Crystal structure of the bacillus subtilis ykui protein, with an eal domain. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BAS
- Type
- protein
- Length
- 799 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ykui protein
- UniProt
- O35014
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ykui protein | protein | 402 | 42% helix, 24% strand | O35014 |
| B | Ykui protein | protein | 397 | 41% helix, 23% strand | O35014 |
Ligands and binding sites
- BME · Beta-mercaptoethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.87 | 0.88 | 106 | empty |
| 2 | 450 | 0.73 | 0.83 | 46 | empty |
| 3 | 564 | 0.69 | 0.78 | 54 | empty |
| 4 | 395 | 0.64 | 0.78 | 35 | empty |
| 5 | 122 | 0.47 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3206 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 modified, 1 covalent (engineered, additive adduct).
Compared structures
- 2BAS · Crystal Structure of the Bacillus subtilis YkuI Protein, with an EAL Domain. · 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 2BAS · PDBe 2BAS · UniProt O35014
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