Research workbench
Structure of human dicer platform-paz-connector helix cassette in complex with 17-mer siRNA having 5'-P and uu-3' ends (3.1 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
- 4NGF
- Type
- protein + RNA
- Length
- 1,105 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoribonuclease dicer; 5'-R(P*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*UP*U)- 3'
- EC
- 3.1.26.-
- UniProt
- Q9UPY3
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoribonuclease dicer (EC 3.1.26.-) | protein | 260 | 26% helix, 26% strand | Q9UPY3 |
| B | Endoribonuclease dicer (EC 3.1.26.-) | protein | 259 | 27% helix, 25% strand | Q9UPY3 |
| C | Endoribonuclease dicer (EC 3.1.26.-) | protein | 258 | 25% helix, 28% strand | Q9UPY3 |
| D | Endoribonuclease dicer (EC 3.1.26.-) | protein | 260 | 26% helix, 25% strand | Q9UPY3 |
| E, F, G, H | 5'-R(P*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*UP*U)- 3' | rna | 17 | — | — |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.70 | 0.83 | 41 | empty |
| 2 | 429 | 0.70 | 0.81 | 58 | empty |
| 3 | 295 | 0.69 | 0.84 | 44 | empty |
| 4 | 301 | 0.63 | 0.80 | 49 | empty |
| 5 | 83 | 0.61 | 0.89 | 20 | empty |
Interfaces
10 interfaces between chains.
- E–F · 703 Ų buried · 76 hydrogen bonds · nucleic-nucleic
- G–H · 698 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- A–H · 669 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–E · 668 Ų buried · 21 hydrogen bonds · protein-nucleic
- D–G · 653 Ų buried · 21 hydrogen bonds · protein-nucleic
Compared structures
- 4NGF · Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 17-mer… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9UPY3 · AlphaFold monomer V2.0 prediction for endoribonuclease dicer (Q9UPY3) · a predicted model of the same protein · chain D against A, TM-score 0.88
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 4NGF · PDBe 4NGF · UniProt Q9UPY3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.