Research workbench
Crystal structure of the S. cerevisiae YDR533C protein
Analyse Crystal structure of the S. cerevisiae YDR533C protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QVV
- Type
- protein
- Length
- 940 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YDR533C protein
- UniProt
- Q04432
- Pockets
- 6 · best druggability 0.46
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | YDR533C protein | protein | 234 | 41% helix, 17% strand | Q04432 |
| B | YDR533C protein | protein | 237 | 41% helix, 16% strand | Q04432 |
| C | YDR533C protein | protein | 235 | 41% helix, 16% strand | Q04432 |
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.46 | 0.74 | 26 | empty |
| 2 | 75 | 0.34 | 0.76 | 17 | empty |
| 3 | 66 | 0.34 | 0.76 | 20 | empty |
| 4 | 50 | 0.32 | 0.77 | 14 | empty |
| 5 | 64 | 0.31 | 0.75 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–D · 220 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 206 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 201 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 26 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (artifact).
Compared structures
- 1QVV · Crystal structure of the S. cerevisiae YDR533c protein · the same entry in another collection · chain A against A, TM-score 1.00
- Q04432 · AlphaFold monomer V2.0 prediction for glutathione-independent glyoxalase HSP31 (Q04432) · a predicted model of the same protein · chain A 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 Q04432
- Elsewhere: RCSB PDB 1QVV · PDBe 1QVV · UniProt Q04432
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