MolNFT v1 · #75173 · protein
Crystal structure of the 5'->3' exoribonuclease XRN1, E178Q mutant
3PIE · 5'->3' exoribonuclease (XRN1): “Crystal structure of the 5'->3' exoribonuclease XRN1, E178Q mutant”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #75173 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3PIE
- Type
- protein
- Length
- 4,202 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'->3' exoribonuclease (XRN1)
- UniProt
- Q6CJ09
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'->3' exoribonuclease (XRN1) | protein | 1057 | 39% helix, 18% strand | Q6CJ09 |
| B | 5'->3' exoribonuclease (XRN1) | protein | 1056 | 39% helix, 18% strand | Q6CJ09 |
| C | 5'->3' exoribonuclease (XRN1) | protein | 1066 | 37% helix, 17% strand | Q6CJ09 |
| D | 5'->3' exoribonuclease (XRN1) | protein | 1023 | 37% helix, 17% strand | Q6CJ09 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.84 | 0.85 | 92 | empty |
| 2 | 1042 | 0.84 | 0.85 | 100 | empty |
| 3 | 1133 | 0.83 | 0.84 | 110 | empty |
| 4 | 1178 | 0.79 | 0.80 | 96 | empty |
| 5 | 161 | 0.73 | 0.91 | 33 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1454 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1423 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 298 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 165 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3PIE · Crystal structure of the 5'->3' exoribonuclease Xrn1, E178Q mutant · the same entry in another collection · chain C against C, TM-score 1.00
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 Q6CJ09
- Elsewhere: RCSB PDB 3PIE · PDBe 3PIE · UniProt Q6CJ09
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