Research workbench
The hapten triclocarban bound to the single domain camelid nanobody vhh T10
Analyse The hapten triclocarban bound to the single domain camelid nanobody vhh T10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VM6
- Type
- protein
- Length
- 129 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single domain camelid nanobody vhh T10
- Ligands
- 9EG, NA, SO4
- Pockets
- 1 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single domain camelid nanobody vhh T10 | protein | 129 | 9% helix, 47% strand | — |
Ligands and binding sites
- 9EG · N-(4-chlorophenyl)-N'-(3,4-dichlorophenyl)urea · ligand · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.57 | 0.89 | 20 | 9EG |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5VM6 · The hapten triclocarban bound to the single domain camelid nanobody VHH T10 · 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 5VM6 · PDBe 5VM6
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