Research workbench
Cryo-EM structure of arabidopsis DCL3 in complex with a 40-bp RNA
Analyse Cryo-EM structure of arabidopsis DCL3 in complex with a 40-bp RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VG2
- Type
- protein + RNA
- Length
- 916 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dicer-like 3; TAS1A forward strand (5'-phosphorylation); TAS1A reverse strand
- UniProt
- F4J0I5
- Ligands
- CA, ZN
- Pockets
- 11 · best druggability 0.80
Structure
electron microscopy · 3 distinct chains · 38% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dicer-like 3 | protein | 845 | 38% helix, 13% strand | F4J0I5 |
| C | TAS1A forward strand (5'-phosphorylation) | rna | 35 | — | — |
| D | TAS1A reverse strand | rna | 36 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.80 | 0.87 | 43 | empty |
| 2 | 1183 | 0.80 | 0.82 | 76 | empty |
| 3 | 811 | 0.79 | 0.83 | 72 | empty |
| 4 | 54 | 0.63 | 0.94 | 21 | empty |
| 5 | 89 | 0.56 | 0.87 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–D · 2358 Ų buried · 35 hydrogen bonds · protein-nucleic
- A–C · 1978 Ų buried · 37 hydrogen bonds · protein-nucleic
- C–D · 1625 Ų buried · 141 hydrogen bonds · nucleic-nucleic
Compared structures
- 7VG2 · Cryo-EM structure of Arabidopsis DCL3 in complex with a 40-bp RNA · 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 F4J0I5
- Elsewhere: RCSB PDB 7VG2 · PDBe 7VG2 · UniProt F4J0I5
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