Research workbench
The structural basis of histone CHAPERONEVPS75
Analyse The structural basis of histone CHAPERONEVPS75 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YPS
- Type
- protein
- Length
- 1,206 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 75
- UniProt
- A0A0W4ZF97
- Ligands
- CA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 75 | protein | 202 | 50% helix, 14% strand | A0A0W4ZF97 |
| B, D | Vacuolar protein sorting-associated protein 75 | protein | 200 | 48% helix, 14% strand | A0A0W4ZF97 |
| C, F | Vacuolar protein sorting-associated protein 75 | protein | 201 | 45% helix, 14% strand | A0A0W4ZF97 |
| E | Vacuolar protein sorting-associated protein 75 | protein | 202 | 46% helix, 13% strand | A0A0W4ZF97 |
Ligands and binding sites
- CA · Calcium ion · metal · 12 copies · chains A, D, B, C, E, F
- 1PE · Pentaethylene glycol · additive · 19 copies · chains A, B, E, D, C, F
- GOL · Glycerol · additive · 13 copies · chains A, B, D, C, E, F
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, D, B, E, F
- PGE · Triethylene glycol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.83 | 0.84 | 88 | 1PE |
| 2 | 519 | 0.81 | 0.88 | 74 | empty |
| 3 | 356 | 0.76 | 0.86 | 54 | 1PE, GOL |
| 4 | 401 | 0.75 | 0.85 | 49 | empty |
| 5 | 285 | 0.74 | 0.87 | 38 | 1PE, PEG |
Interfaces
9 interfaces between chains.
- A–B · 1888 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1792 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1706 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 1439 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1430 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 5YPS · The structural basis of histone chaperoneVps75 · the same entry in another collection · 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 A0A0W4ZF97
- Elsewhere: RCSB PDB 5YPS · PDBe 5YPS · UniProt A0A0W4ZF97
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