Research workbench
Canine parvovirus strain D empty capsid structure at pH 5.5
Analyse Canine parvovirus strain D empty capsid structure at pH 5.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C8H
- Type
- protein
- Length
- 544 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Canine parvovirus capsid
- Ligands
- CA
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Canine parvovirus capsid | protein | 544 | 8% helix, 29% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.71 | 0.78 | 74 | empty |
| 2 | 58 | 0.69 | 0.97 | 15 | empty |
| 3 | 90 | 0.66 | 0.91 | 20 | empty |
| 4 | 453 | 0.57 | 0.74 | 35 | empty |
| 5 | 240 | 0.52 | 0.76 | 34 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1C8H · Canine parvovirus strain D empty capsid structure at pH 5.5 · 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 1C8H · PDBe 1C8H
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