MolNFT v1 · #31919 · protein
Crystal structure of the bacillus subtilis ykui protein, with an eal domain.
2BAS: “Crystal structure of the bacillus subtilis ykui protein, with an eal domain.”. X-ray diffraction, 8 pockets (best druggability 0.87). MolNFT v1 #31919 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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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