Research workbench
Crystal structure of yeast FSH1/YHR049W, a member of the serine hydrolase family
Analyse Crystal structure of yeast FSH1/YHR049W, a member of the serine hydrolase family in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YCD
- Type
- protein
- Length
- 475 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical 27.3 kda protein in AAP1-SMF2 intergenic region
- UniProt
- P38777
- Ligands
- LI5
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical 27.3 kda protein in AAP1-SMF2 intergenic region | protein | 237 | 39% helix, 18% strand | P38777 |
| B | Hypothetical 27.3 kda protein in AAP1-SMF2 intergenic region | protein | 238 | 39% helix, 18% strand | P38777 |
Ligands and binding sites
- LI5 · 2-hydroxy-4,5-dioxoheptyl hydrogen phosphonate · ligand · 2 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 | 255 | 0.63 | 0.81 | 35 | empty |
| 2 | 159 | 0.50 | 0.78 | 29 | LI5 |
| 3 | 153 | 0.47 | 0.77 | 26 | LI5 |
Interfaces
1 interface between chains.
- A–B · 335 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1YCD · Crystal structure of yeast FSH1/YHR049W, a member of the serine hydrolase family · the same entry in another collection · chain A against A, TM-score 1.00
- P38777 · AlphaFold monomer V2.0 prediction for family of serine hydrolases 1 (P38777) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 P38777
- Elsewhere: RCSB PDB 1YCD · PDBe 1YCD · UniProt P38777
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