Research workbench
Crystal structure of yeast VPS74-N-term truncation variant
Analyse Crystal structure of yeast VPS74-N-term truncation variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZII
- Type
- protein
- Length
- 1,124 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 74
- UniProt
- Q06385
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 74 | protein | 281 | 53% helix, 7% strand | Q06385 |
| B | Vacuolar protein sorting-associated protein 74 | protein | 281 | 48% helix, 7% strand | Q06385 |
| C | Vacuolar protein sorting-associated protein 74 | protein | 279 | 50% helix, 8% strand | Q06385 |
| D | Vacuolar protein sorting-associated protein 74 | protein | 283 | 53% helix, 6% strand | Q06385 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.87 | 0.88 | 135 | empty |
| 2 | 485 | 0.73 | 0.82 | 48 | empty |
| 3 | 68 | 0.48 | 0.84 | 19 | empty |
| 4 | 65 | 0.38 | 0.79 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1337 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 1004 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 987 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 820 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 752 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2ZII · Crystal Structure of Yeast Vps74-N-term Truncation Variant · the same entry in another collection · chain D against D, TM-score 1.00
- Q06385 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 74… · 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 Q06385
- Elsewhere: RCSB PDB 2ZII · PDBe 2ZII · UniProt Q06385
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