Research workbench
Crystal structure of dicer from giardia intestinalis
Analyse Crystal structure of dicer from giardia intestinalis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FFL
- Type
- protein
- Length
- 2,896 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dicer
- EC
- 3.1.26.3
- Ligands
- MN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dicer (EC 3.1.26.3) | protein | 732 | 48% helix, 12% strand | — |
| B | Dicer (EC 3.1.26.3) | protein | 726 | 51% helix, 12% strand | — |
| C | Dicer (EC 3.1.26.3) | protein | 718 | 50% helix, 11% strand | — |
| D | Dicer (EC 3.1.26.3) | protein | 720 | 52% helix, 12% strand | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 39 copies · chains A, D, B, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.87 | 0.90 | 123 | MN |
| 2 | 951 | 0.87 | 0.88 | 99 | MN |
| 3 | 437 | 0.80 | 0.89 | 59 | MN |
| 4 | 1058 | 0.76 | 0.78 | 87 | MN |
| 5 | 251 | 0.59 | 0.79 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1349 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1193 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 391 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2FFL · Crystal Structure of Dicer from Giardia intestinalis · 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
- Elsewhere: RCSB PDB 2FFL · PDBe 2FFL
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