Research workbench
Crystal structure of the chimeric archaeoglobus fulgidus RNA splicing endonuclease with the broadest substrate specificity
Analyse Crystal structure of the chimeric archaeoglobus fulgidus RNA splicing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P1Y
- Type
- protein
- Length
- 1,256 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA-splicing endonuclease
- EC
- 3.1.27.9
- UniProt
- O29362, Q9YBF1
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | TRNA-splicing endonuclease (EC 3.1.27.9) | protein | 314 | 32% helix, 27% strand | O29362, Q9YBF1 |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 760 | 0.81 | 0.84 | 96 | empty |
| 2 | 738 | 0.80 | 0.84 | 98 | empty |
| 3 | 525 | 0.76 | 0.84 | 59 | empty |
| 4 | 486 | 0.76 | 0.84 | 59 | empty |
| 5 | 55 | 0.49 | 0.86 | 13 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3444 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 3398 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 763 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 472 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3P1Y · Crystal structure of the chimeric Archaeoglobus fulgidus RNA splicing endonuclease with… · the same entry in another collection · chain A against A, TM-score 1.00
- O29362 · AlphaFold monomer V2.0 prediction for tRNA-splicing endonuclease (O29362) · a predicted model of the same protein · chain D against A, TM-score 0.96
- Q9YBF1 · AlphaFold monomer V2.0 prediction for tRNA-splicing endonuclease (Q9YBF1) · a predicted model of the same protein · chain B against A, TM-score 0.50
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 O29362
- Every structure of UniProt Q9YBF1
- Elsewhere: RCSB PDB 3P1Y · PDBe 3P1Y · UniProt O29362 · UniProt Q9YBF1
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