MolNFT v1 · #51749 · protein
Structure of S. cerevisiae DOM34, a translation termination-like factor involved in RNA quality control pathways and interacting with HBS1 (selenomet-labeled protein)
2VGN: “Structure of S. cerevisiae DOM34, a translation termination-like factor involved in RNA quality control…”. X-ray diffraction, 1 ligand (PO4), 7 pockets (best druggability 0.80). MolNFT v1 #51749 on GenesisL1: 3D structure, binding…
- PDB
- 2VGN
- Type
- protein
- Length
- 716 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DOM34
- UniProt
- P33309
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DOM34 | protein | 360 | 35% helix, 29% strand | P33309 |
| B | DOM34 | protein | 356 | 36% helix, 29% strand | P33309 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.80 | 0.82 | 93 | empty |
| 2 | 780 | 0.79 | 0.82 | 67 | GOL |
| 3 | 92 | 0.44 | 0.80 | 15 | empty |
| 4 | 82 | 0.43 | 0.79 | 20 | empty |
| 5 | 76 | 0.40 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1207 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 2VGN · Structure of S. cerevisiae Dom34, a translation termination-like factor involved in RNA… · the same entry in another collection · chain A against A, TM-score 1.00
- P33309 · AlphaFold monomer V2.0 prediction for protein DOM34 (P33309) · a predicted model of the same protein · chain B against A, TM-score 0.71
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 P33309
- Elsewhere: RCSB PDB 2VGN · PDBe 2VGN · UniProt P33309
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