Research workbench
Desmodium yellow mottle tymovirus
Analyse Desmodium yellow mottle tymovirus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DDL
- Type
- protein + RNA
- Length
- 560 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3'); RNA (5'-R(P*UP*U)-3'); Desmodium yellow mottle virus
- UniProt
- O89511
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3') | rna | 7 | — | — |
| E | RNA (5'-R(P*UP*U)-3') | rna | 2 | — | — |
| A, B | Desmodium yellow mottle virus | protein | 188 | 9% helix, 43% strand | O89511 |
| C | Desmodium yellow mottle virus | protein | 175 | 9% helix, 45% strand | O89511 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.60 | 0.76 | 57 | empty |
| 2 | 56 | 0.51 | 0.87 | 20 | empty |
| 3 | 72 | 0.49 | 0.84 | 25 | empty |
| 4 | 135 | 0.45 | 0.77 | 27 | empty |
| 5 | 88 | 0.39 | 0.77 | 19 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2072 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 2009 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1422 Ų buried · 27 hydrogen bonds · protein-protein
- E–A · 407 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–B · 336 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 1DDL · Desmodium yellow mottle tymovirus · the same entry in another collection · chain D against D, 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 O89511
- Elsewhere: RCSB PDB 1DDL · PDBe 1DDL · UniProt O89511
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