MolNFT v1 · #120262 · protein + RNA
Crystal structure of silkworm piwi-clade argonaute siwi bound to pirna
5GUH: “Crystal structure of silkworm piwi-clade argonaute siwi bound to pirna”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.68). MolNFT v1 #120262 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GUH
- Type
- protein + RNA
- Length
- 767 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Piwi; RNA (28-mer)
- UniProt
- A8D8P8
- Ligands
- MG
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Piwi | protein | 759 | 32% helix, 29% strand | A8D8P8 |
| B | RNA (28-mer) | rna | 8 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 654 | 0.68 | 0.77 | 65 | empty |
| 2 | 364 | 0.61 | 0.77 | 52 | empty |
| 3 | 215 | 0.56 | 0.79 | 21 | empty |
| 4 | 100 | 0.38 | 0.75 | 25 | empty |
| 5 | 87 | 0.37 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1103 Ų buried · 39 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5GUH · Crystal structure of silkworm PIWI-clade Argonaute Siwi bound to piRNA · the same entry in another collection · chain A against A, TM-score 1.00
- A8D8P8 · AlphaFold monomer V2.0 prediction for piwi-like protein siwi (A8D8P8) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 A8D8P8
- Elsewhere: RCSB PDB 5GUH · PDBe 5GUH · UniProt A8D8P8
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