MolNFT v1 · #109306 · protein
Crystal structure of the dicer-trbp interface
4WYQ · Endoribonuclease dicer: “Crystal structure of the dicer-trbp interface”. X-ray diffraction, 6 pockets (best druggability 0.74). MolNFT v1 #109306 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WYQ
- Type
- protein
- Length
- 410 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoribonuclease dicer; Risc-loading complex subunit TARBP2; POLY(UNK)
- EC
- 3.1.26.3
- UniProt
- Q9UPY3, Q15633
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Endoribonuclease dicer (EC 3.1.26.3) | protein | 119 | 73% helix, 0% strand | Q9UPY3 |
| B, E | Risc-loading complex subunit TARBP2 | protein | 75 | 41% helix, 27% strand | Q15633 |
| C, F | POLY(UNK) | protein | 11 | 45% helix, 0% strand | — |
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 | 216 | 0.74 | 0.89 | 36 | empty |
| 2 | 152 | 0.50 | 0.78 | 27 | empty |
| 3 | 109 | 0.46 | 0.79 | 28 | empty |
| 4 | 76 | 0.41 | 0.79 | 22 | empty |
| 5 | 95 | 0.40 | 0.77 | 15 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1064 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1060 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 515 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 319 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 304 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4WYQ · Crystal structure of the Dicer-TRBP interface · the same entry in another collection · chain F against F, TM-score 1.00
- Q15633 · AlphaFold monomer V2.0 prediction for risc-loading complex subunit TARBP2 (Q15633) · a predicted model of the same protein · chain B against A, TM-score 0.96
- Q9UPY3 · AlphaFold monomer V2.0 prediction for endoribonuclease dicer (Q9UPY3) · a predicted model of the same protein · chain D against A, TM-score 0.78
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
- Every structure of UniProt Q15633
- Elsewhere: RCSB PDB 4WYQ · PDBe 4WYQ · UniProt Q9UPY3 · UniProt Q15633
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