MolNFT v1 · #141512 · protein + RNA
Arabidopsis small RNA degrading nuclease 1 in complex with an RNA substrate
5Z9X: “Arabidopsis small RNA degrading nuclease 1 in complex with an RNA substrate”. X-ray diffraction, 2 ligands (MG, SO4), 6 pockets (best druggability 0.67). MolNFT v1 #141512 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5Z9X
- Type
- protein + RNA
- Length
- 297 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small RNA degrading nuclease 1; RNA (5'-R(P*GP*CP*CP*CP*AP*UP*UP*AP*G)-3')
- EC
- 3.1.-.-
- UniProt
- A3KPE8
- Ligands
- MG, SO4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Small RNA degrading nuclease 1 (EC 3.1.-.-) | protein | 288 | 45% helix, 14% strand | A3KPE8 |
| R | RNA (5'-R(P*GP*CP*CP*CP*AP*UP*UP*AP*G)-3') | rna | 9 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.67 | 0.94 | 21 | empty |
| 2 | 88 | 0.49 | 0.82 | 19 | empty |
| 3 | 157 | 0.49 | 0.77 | 26 | empty |
| 4 | 53 | 0.42 | 0.83 | 16 | empty |
| 5 | 181 | 0.41 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–R · 599 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 5Z9X · Arabidopsis SMALL RNA DEGRADING NUCLEASE 1 in complex with an RNA substrate · the same entry in another collection · chain A against A, TM-score 1.00
- A3KPE8 · AlphaFold monomer V2.0 prediction for small RNA degrading nuclease 1 (A3KPE8) · 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 A3KPE8
- Elsewhere: RCSB PDB 5Z9X · PDBe 5Z9X · UniProt A3KPE8
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