Research workbench
Crystal structure of a vhh against the capsid protein from blv
Analyse Crystal structure of a vhh against the capsid protein from blv in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OC8
- Type
- protein
- Length
- 486 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VHH8C
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VHH8C | protein | 121 | 12% helix, 44% strand | — |
| B | VHH8C | protein | 123 | 11% helix, 45% strand | — |
| C | VHH8C | protein | 122 | 11% helix, 45% strand | — |
| D | VHH8C | protein | 120 | 12% helix, 43% 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.68 | 0.73 | 85 | empty |
| 2 | 52 | 0.26 | 0.73 | 12 | empty |
Interfaces
4 interfaces between chains.
- A–B · 392 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 386 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 371 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 360 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6OC8 · Crystal structure of a VHH against the capsid protein from BLV · 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 6OC8 · PDBe 6OC8
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