Research workbench
Crystal structure of carboxylesterase cesb (ybfk) from bacillus subtilis
Analyse Crystal structure of carboxylesterase cesb (ybfk) 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
- 4CCY
- Type
- protein
- Length
- 570 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxylesterase ybfk
- EC
- 3.1.1.1
- UniProt
- O31452
- Ligands
- NA
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carboxylesterase ybfk (EC 3.1.1.1) | protein | 285 | 44% helix, 19% strand | O31452 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.86 | 0.87 | 114 | empty |
| 2 | 112 | 0.43 | 0.78 | 18 | empty |
| 3 | 109 | 0.41 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 612 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 4CCY · Crystal structure of carboxylesterase CesB (YbfK) from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- O31452 · AlphaFold monomer V2.0 prediction for carboxylesterase ybfk (O31452) · 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 O31452
- Elsewhere: RCSB PDB 4CCY · PDBe 4CCY · UniProt O31452
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