MolNFT v1 · #35423 · protein
Crystal structure of the C-terminal RNase III domain of human dicer
2EB1 · Endoribonuclease dicer: “Crystal structure of the C-terminal RNase III domain of human dicer”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.64). MolNFT v1 #35423 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2EB1
- Type
- protein
- Length
- 510 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoribonuclease dicer
- EC
- 3.1.26.3
- UniProt
- Q9UPY3
- Ligands
- MG
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoribonuclease dicer (EC 3.1.26.3) | protein | 171 | 67% helix, 1% strand | Q9UPY3 |
| B | Endoribonuclease dicer (EC 3.1.26.3) | protein | 170 | 68% helix, 1% strand | Q9UPY3 |
| C | Endoribonuclease dicer (EC 3.1.26.3) | protein | 169 | 69% helix, 1% strand | Q9UPY3 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.64 | 0.93 | 15 | empty |
| 2 | 210 | 0.55 | 0.79 | 30 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1326 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 698 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2EB1 · Crystal Structure of the C-Terminal RNase III Domain of Human Dicer · 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 C against A, TM-score 0.98
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 2EB1 · PDBe 2EB1 · UniProt Q9UPY3
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