Research workbench
X-ray crystal structure of yeast RNA triphosphatase in complex with sulfate and manganese ions.
Analyse X-ray crystal structure of yeast RNA triphosphatase in complex with sulfate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D8H
- Type
- protein
- Length
- 864 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA triphosphatase CET1
- EC
- 3.1.3.33
- UniProt
- O13297
- Ligands
- MN, SO4
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | MRNA triphosphatase CET1 (EC 3.1.3.33) | protein | 288 | 27% helix, 35% strand | O13297 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.84 | 0.87 | 83 | empty |
| 2 | 876 | 0.76 | 0.79 | 92 | MN, SO4 |
| 3 | 256 | 0.61 | 0.80 | 25 | empty |
| 4 | 381 | 0.57 | 0.76 | 44 | SO4 |
| 5 | 273 | 0.56 | 0.78 | 33 | MN, SO4 |
Interfaces
2 interfaces between chains.
- A–B · 2229 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 621 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1D8H · X-ray crystal structure of yeast RNA triphosphatase in complex with sulfate and manganese… · the same entry in another collection · chain A against A, TM-score 1.00
- O13297 · AlphaFold monomer V2.0 prediction for mRNA-capping enzyme subunit beta (O13297) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O13297
- Elsewhere: RCSB PDB 1D8H · PDBe 1D8H · UniProt O13297
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