Research workbench
Structure of human dicer platform-paz-connector helix cassette in complex with 13-mer siRNA having 5'-a and uu-3' ends (2.6 ångström resolution)
Analyse Structure of human dicer platform-paz-connector helix cassette in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NGG
- Type
- protein + RNA
- Length
- 280 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoribonuclease dicer; 5'-R(*AP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'
- EC
- 3.1.26.-
- UniProt
- Q9UPY3
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoribonuclease dicer (EC 3.1.26.-) | protein | 267 | 27% helix, 27% strand | Q9UPY3 |
| B | 5'-R(*AP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3' | rna | 13 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.66 | 0.80 | 49 | PO4 |
| 2 | 326 | 0.52 | 0.73 | 40 | empty |
| 3 | 106 | 0.44 | 0.78 | 21 | empty |
| 4 | 74 | 0.34 | 0.75 | 14 | empty |
| 5 | 50 | 0.28 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 396 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 4NGG · Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 13-mer… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UPY3 · AlphaFold monomer V2.0 prediction for endoribonuclease dicer (Q9UPY3) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 Q9UPY3
- Elsewhere: RCSB PDB 4NGG · PDBe 4NGG · UniProt Q9UPY3
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