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Crystal structure of the 5'->3' exoribonuclease XRN1, E178Q mutant in complex with manganese
Analyse Crystal structure of the 5'->3' exoribonuclease XRN1, E178Q mutant in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PIF
- 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
- Ligands
- MN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'->3' exoribonuclease (XRN1) | protein | 1057 | 40% helix, 18% strand | Q6CJ09 |
| B | 5'->3' exoribonuclease (XRN1) | protein | 1056 | 39% helix, 18% strand | Q6CJ09 |
| C | 5'->3' exoribonuclease (XRN1) | protein | 1066 | 38% helix, 17% strand | Q6CJ09 |
| D | 5'->3' exoribonuclease (XRN1) | protein | 1023 | 37% helix, 18% strand | Q6CJ09 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 978 | 0.84 | 0.85 | 106 | empty |
| 2 | 964 | 0.84 | 0.85 | 88 | empty |
| 3 | 1088 | 0.83 | 0.84 | 102 | empty |
| 4 | 1153 | 0.82 | 0.83 | 118 | empty |
| 5 | 976 | 0.72 | 0.76 | 83 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1446 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1425 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 295 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 162 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3PIF · Crystal structure of the 5'->3' exoribonuclease Xrn1, E178Q mutant in Complex with… · the same entry in another collection · chain B against B, 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 3PIF · PDBe 3PIF · UniProt Q6CJ09
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