Research workbench
Crystal structure of orsay virus delta protein N-terminal fragment (aa 1-101)
Analyse Crystal structure of orsay virus delta protein N-terminal fragment (aa 1-101) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W82
- Type
- protein
- Length
- 504 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein delta
- UniProt
- E9KNV6
- Pockets
- 4 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B, D, E | Protein delta | protein | 101 | 43% helix, 31% strand | E9KNV6 |
| A | Protein delta | protein | 100 | 43% helix, 31% strand | E9KNV6 |
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.88 | 0.95 | 70 | empty |
| 2 | 72 | 0.76 | 0.98 | 20 | empty |
| 3 | 70 | 0.75 | 0.97 | 20 | empty |
| 4 | 63 | 0.73 | 0.96 | 20 | empty |
Interfaces
10 interfaces between chains.
- C–D · 3402 Ų buried · 53 hydrogen bonds · protein-protein
- E–A · 3347 Ų buried · 55 hydrogen bonds · protein-protein
- C–B · 3330 Ų buried · 50 hydrogen bonds · protein-protein
- B–A · 3329 Ų buried · 53 hydrogen bonds · protein-protein
- D–E · 3321 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 5W82 · Crystal structure of Orsay virus delta protein N-terminal fragment (aa 1-101) · the same entry in another collection · chain C against C, 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 E9KNV6
- Elsewhere: RCSB PDB 5W82 · PDBe 5W82 · UniProt E9KNV6
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