Research workbench
Crystal structure of a putative serine hydrolase (YDR428C) from saccharomyces cerevisiae at 1.85 a resolution
Analyse Crystal structure of a putative serine hydrolase (YDR428C) from saccharomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VKH
- Type
- protein
- Length
- 513 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative serine hydrolase
- UniProt
- Q04066
- Ligands
- CL
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative serine hydrolase | protein | 261 | 46% helix, 16% strand | Q04066 |
| B | Putative serine hydrolase | protein | 252 | 47% helix, 17% strand | Q04066 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.52 | 0.79 | 23 | empty |
| 2 | 156 | 0.51 | 0.79 | 26 | empty |
| 3 | 69 | 0.46 | 0.82 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 894 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 1VKH · Crystal structure of a putative serine hydrolase (YDR428C) from saccharomyces cerevisiae… · the same entry in another collection · chain A against A, TM-score 1.00
- Q04066 · AlphaFold monomer V2.0 prediction for kynurenine formamidase (Q04066) · 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 Q04066
- Elsewhere: RCSB PDB 1VKH · PDBe 1VKH · UniProt Q04066
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