Research workbench
GII.17 KAWASAKI323 protruding domain in complex with nanobody nano-4
Analyse GII.17 KAWASAKI323 protruding domain in complex with nanobody nano-4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O02
- Type
- protein
- Length
- 428 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Nanobody (vhh) nano-4
- UniProt
- A0A0A7CJV4
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 304 | 6% helix, 35% strand | A0A0A7CJV4 |
| C | Nanobody (vhh) nano-4 | protein | 124 | 10% helix, 50% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.42 | 0.75 | 25 | empty |
| 2 | 51 | 0.28 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–C · 559 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5O02 · GII.17 Kawasaki323 protruding domain in complex with Nanobody Nano-4 · 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 A0A0A7CJV4
- Elsewhere: RCSB PDB 5O02 · PDBe 5O02 · UniProt A0A0A7CJV4
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