Research workbench
Crystal structure of ytaa (2635576) from bacillus subtilis at 2.50 a resolution
Analyse Crystal structure of ytaa (2635576) from bacillus subtilis at 2.50 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q83
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ytaa protein
- UniProt
- O34656
- Ligands
- ADN, UNL, SO4
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ytaa protein | protein | 332 | 53% helix, 13% strand | O34656 |
| B | Ytaa protein | protein | 332 | 54% helix, 12% strand | O34656 |
Ligands and binding sites
- ADN · Adenosine · ligand · 2 copies · chains A, B
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- CIT · Citric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.80 | 0.87 | 49 | empty |
| 2 | 124 | 0.47 | 0.78 | 21 | ADN |
| 3 | 115 | 0.47 | 0.78 | 18 | ADN |
| 4 | 80 | 0.46 | 0.81 | 14 | empty |
| 5 | 89 | 0.44 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 759 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 2Q83 · Crystal structure of ytaA (2635576) from Bacillus subtilis at 2.50 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- O34656 · AlphaFold monomer V2.0 prediction for spore coat protein I (O34656) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O34656
- Elsewhere: RCSB PDB 2Q83 · PDBe 2Q83 · UniProt O34656
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