Research workbench
Crystal structure of israel acute paralysis virus pentamer
Analyse Crystal structure of israel acute paralysis virus pentamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CDD
- Type
- protein
- Length
- 709 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural polyprotein, VP1; Structural polyprotein, VP3; Structural polyprotein, VP2
- UniProt
- B3TZF1, D1FK67
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Structural polyprotein, VP1 | protein | 208 | 17% helix, 36% strand | B3TZF1 |
| B | Structural polyprotein, VP3 | protein | 301 | 6% helix, 35% strand | D1FK67 |
| C | Structural polyprotein, VP2 | protein | 200 | 13% helix, 37% strand | D1FK67 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.62 | 0.85 | 26 | empty |
| 2 | 200 | 0.52 | 0.77 | 30 | empty |
| 3 | 75 | 0.50 | 0.84 | 18 | empty |
| 4 | 177 | 0.50 | 0.77 | 22 | empty |
| 5 | 81 | 0.43 | 0.80 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4515 Ų buried · 68 hydrogen bonds · protein-protein
- B–C · 1571 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1312 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5CDD · Crystal Structure of Israel acute Paralysis Virus Pentamer · 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 B3TZF1
- Every structure of UniProt D1FK67
- Elsewhere: RCSB PDB 5CDD · PDBe 5CDD · UniProt B3TZF1 · UniProt D1FK67
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