Research workbench
Crystal structure of a putative lipoprotein (ycda) from bacillus subtilis subsp. subtilis str. 168 at 2.62 a resolution
Analyse Crystal structure of a putative lipoprotein (ycda) from bacillus subtilis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R4G
- Type
- protein
- Length
- 322 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative lipoprotein ycda
- UniProt
- O34538
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative lipoprotein ycda | protein | 322 | 37% helix, 30% strand | O34538 |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.56 | 0.77 | 29 | PG4 |
| 2 | 183 | 0.53 | 0.78 | 26 | empty |
| 3 | 79 | 0.33 | 0.75 | 25 | PG4 |
| 4 | 66 | 0.31 | 0.74 | 15 | empty |
| 5 | 56 | 0.29 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 4R4G · Crystal structure of a putative lipoprotein (ycdA) from Bacillus subtilis subsp. subtilis… · the same entry in another collection · chain A against A, TM-score 1.00
- O34538 · AlphaFold monomer V2.0 prediction for uncharacterized lipoprotein ycda (O34538) · 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 O34538
- Elsewhere: RCSB PDB 4R4G · PDBe 4R4G · UniProt O34538
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