MolNFT v2 · #225743 · protein
Cryo EM structure of Komagataella phaffii Rat1-Rai1-Rtt103 complex
8YF5 · 5'-3' exoribonuclease: “Cryo EM structure of Komagataella phaffii Rat1-Rai1-Rtt103 complex”. Electron microscopy at 3.78, 20 pockets (best druggability 0.82). MolNFT v2 #225743 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 8YF5
- Type
- protein
- Length
- 2,250 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.78
- Source
- Komagataella phaffii
- Molecule
- 5'-3' exoribonuclease; Decapping nuclease; Exonuclease Rat1p and Rai1p interacting protein
- EC
- 3.1.13.-, 3.6.1.-
- UniProt
- F2QV79, F2QLF5, F2QNA8
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · resolution 3.78 · 5 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-3' exoribonuclease (EC 3.1.13.-) | protein | 685 | 43% helix, 9% strand | F2QV79 |
| B | Decapping nuclease (EC 3.6.1.-) | protein | 381 | 39% helix, 24% strand | F2QLF5 |
| C | 5'-3' exoribonuclease (EC 3.1.13.-) | protein | 674 | 41% helix, 10% strand | F2QV79 |
| D | Decapping nuclease (EC 3.6.1.-) | protein | 380 | 39% helix, 25% strand | F2QLF5 |
| E | Exonuclease Rat1p and Rai1p interacting protein | protein | 130 | 78% helix, 0% strand | F2QNA8 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.82 | 0.83 | 97 | empty |
| 2 | 1066 | 0.81 | 0.82 | 95 | empty |
| 3 | 954 | 0.80 | 0.82 | 82 | empty |
| 4 | 851 | 0.80 | 0.82 | 102 | empty |
| 5 | 1156 | 0.77 | 0.79 | 73 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1581 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1580 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 595 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 539 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 126 Ų buried · 1 hydrogen bond · protein-protein
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 F2QV79
- Every structure of UniProt F2QLF5
- Every structure of UniProt F2QNA8
- Elsewhere: RCSB PDB 8YF5 · PDBe 8YF5 · UniProt F2QV79 · UniProt F2QLF5 · UniProt F2QNA8
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