Research workbench
Structure of human dicer platform-paz-connector helix cassette in complex with 12-mer siRNA having 5'-P and uu-3' ends (1.95 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
- 4NGD
- Type
- protein + RNA
- Length
- 292 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoribonuclease dicer; 5'-R(P*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'
- EC
- 3.1.26.-
- UniProt
- Q9UPY3
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoribonuclease dicer (EC 3.1.26.-) | protein | 280 | 28% helix, 26% strand | Q9UPY3 |
| B | 5'-R(P*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3' | rna | 12 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.74 | 0.83 | 63 | SO4 |
| 2 | 129 | 0.51 | 0.80 | 22 | empty |
| 3 | 135 | 0.38 | 0.73 | 16 | empty |
| 4 | 69 | 0.32 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 551 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 4NGD · Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 12-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 4NGD · PDBe 4NGD · UniProt Q9UPY3
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