Research workbench
Structural basis for 5'-end-specific recognition of the guide RNA strand by the a. fulgidus piwi protein
Analyse Structural basis for 5'-end-specific recognition of the guide RNA strand by the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YTU
- Type
- protein + RNA
- Length
- 856 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(P*AP*GP*AP*CP*AP*G)-3'; 5'-R(P*UP*GP*UP*C)-3'; Hypothetical protein AF1318
- UniProt
- O28951
- Ligands
- MG
- Pockets
- 15 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-R(P*AP*GP*AP*CP*AP*G)-3' | rna | 5 | — | — |
| D, F | 5'-R(P*UP*GP*UP*C)-3' | rna | 4 | — | — |
| E | 5'-R(P*AP*GP*AP*CP*AP*G)-3' | rna | 6 | — | — |
| A | Hypothetical protein AF1318 | protein | 410 | 37% helix, 25% strand | O28951 |
| B | Hypothetical protein AF1318 | protein | 427 | 35% helix, 26% strand | O28951 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains C, A, E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.68 | 0.78 | 42 | empty |
| 2 | 261 | 0.60 | 0.79 | 35 | empty |
| 3 | 92 | 0.50 | 0.82 | 18 | empty |
| 4 | 211 | 0.45 | 0.74 | 23 | empty |
| 5 | 94 | 0.44 | 0.79 | 21 | empty |
Interfaces
8 interfaces between chains.
- A–B · 926 Ų buried · 8 hydrogen bonds · protein-protein
- E–B · 854 Ų buried · 29 hydrogen bonds · protein-nucleic
- C–A · 814 Ų buried · 30 hydrogen bonds · protein-nucleic
- E–F · 213 Ų buried · 14 hydrogen bonds · nucleic-nucleic
- F–B · 212 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 1YTU · Structural basis for 5'-end-specific recognition of the guide RNA strand by the A.… · the same entry in another collection · chain B against B, TM-score 1.00
- O28951 · AlphaFold monomer V2.0 prediction for piwi protein AF_1318 (O28951) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O28951
- Elsewhere: RCSB PDB 1YTU · PDBe 1YTU · UniProt O28951
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