Research workbench
Structure of giardia dicer refined against twinned data
Analyse Structure of giardia dicer refined against twinned data in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QVW
- Type
- protein
- Length
- 2,896 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GLP_546_48378_50642
- EC
- 3.1.26.3
- UniProt
- Q7R2M2
- Ligands
- MN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GLP_546_48378_50642 (EC 3.1.26.3) | protein | 732 | 48% helix, 12% strand | Q7R2M2 |
| B | GLP_546_48378_50642 (EC 3.1.26.3) | protein | 726 | 49% helix, 12% strand | Q7R2M2 |
| C | GLP_546_48378_50642 (EC 3.1.26.3) | protein | 718 | 50% helix, 11% strand | Q7R2M2 |
| D | GLP_546_48378_50642 (EC 3.1.26.3) | protein | 720 | 49% helix, 12% strand | Q7R2M2 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 39 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.85 | 0.89 | 101 | MN |
| 2 | 485 | 0.83 | 0.90 | 65 | MN |
| 3 | 378 | 0.81 | 0.90 | 60 | MN |
| 4 | 937 | 0.78 | 0.80 | 80 | MN |
| 5 | 51 | 0.66 | 0.95 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1264 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1048 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 351 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2QVW · Structure of Giardia Dicer refined against twinned data · the same entry in another collection · chain A against A, TM-score 1.00
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 Q7R2M2
- Elsewhere: RCSB PDB 2QVW · PDBe 2QVW · UniProt Q7R2M2
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