Research workbench
Structure of the VPS75-RTT109 histone chaperone-lysine acetyltransferase complex (full-length proteins in space group P6122)
Analyse Structure of the VPS75-RTT109 histone chaperone-lysine acetyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q66
- Type
- protein
- Length
- 885 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 75; Histone acetyltransferase RTT109
- EC
- 2.3.1.48
- UniProt
- P53853, Q07794
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 75 | protein | 236 | 50% helix, 13% strand | P53853 |
| C | Histone acetyltransferase RTT109 (EC 2.3.1.48) | protein | 432 | 35% helix, 21% strand | Q07794 |
| B | Vacuolar protein sorting-associated protein 75 | protein | 217 | 53% helix, 14% strand | P53853 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.69 | 0.86 | 32 | empty |
| 2 | 306 | 0.60 | 0.78 | 36 | empty |
| 3 | 242 | 0.59 | 0.80 | 30 | empty |
| 4 | 220 | 0.58 | 0.80 | 34 | empty |
| 5 | 243 | 0.58 | 0.79 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1891 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1684 Ų buried · 7 hydrogen bonds · protein-protein
- C–B · 594 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (acetylation).
Compared structures
- 3Q66 · Structure of the Vps75-Rtt109 histone chaperone-lysine acetyltransferase complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P53853 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 75… · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q07794 · AlphaFold monomer V2.0 prediction for histone acetyltransferase RTT109 (Q07794) · a predicted model of the same protein · chain C against A, TM-score 0.88
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 P53853
- Every structure of UniProt Q07794
- Elsewhere: RCSB PDB 3Q66 · PDBe 3Q66 · UniProt P53853 · UniProt Q07794
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