MolNFT v1 · #75865 · protein
Structure of the RTT109-ACCOA/VPS75 complex and implications for chaperone-mediated histone acetylation
3Q33 · Histone acetyltransferase RTT109: “Structure of the RTT109-ACCOA/VPS75 complex and implications for chaperone-mediated histone acetylation”. X-ray diffraction, 2 ligands (ACO, NH2), 11 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 3Q33
- Type
- protein
- Length
- 611 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone acetyltransferase RTT109; Vacuolar protein sorting-associated protein 75; Histone…
- EC
- 2.3.1.48
- UniProt
- Q07794, P53853, P61830
- Ligands
- ACO, NH2
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone acetyltransferase RTT109 (EC 2.3.1.48) | protein | 394 | 30% helix, 22% strand | Q07794 |
| B | Vacuolar protein sorting-associated protein 75 | protein | 213 | 51% helix, 16% strand | P53853 |
| D | Histone H3 | protein | 4 | 0% helix, 0% strand | P61830 |
Ligands and binding sites
- ACO · Acetyl coenzyme *A · ligand · chains A
- NH2 · Amino group · ion · chains A, D
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.73 | 0.85 | 39 | ACO, EDO |
| 2 | 694 | 0.70 | 0.77 | 64 | empty |
| 3 | 313 | 0.68 | 0.82 | 30 | empty |
| 4 | 143 | 0.57 | 0.83 | 24 | empty |
| 5 | 64 | 0.37 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1228 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 205 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 176 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (acetylation).
Compared structures
- 3Q33 · Structure of the Rtt109-AcCoA/Vps75 Complex and Implications for Chaperone-Mediated… · 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 0.96
- Q07794 · AlphaFold monomer V2.0 prediction for histone acetyltransferase RTT109 (Q07794) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P61830 · AlphaFold monomer V2.0 prediction for histone H3 (P61830) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 Q07794
- Every structure of UniProt P53853
- Every structure of UniProt P61830
- Elsewhere: RCSB PDB 3Q33 · PDBe 3Q33 · UniProt Q07794 · UniProt P53853 · UniProt P61830
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