Research workbench
The hapten triclocarban bound to the single domain camelid nanobody vhh T4
Analyse The hapten triclocarban bound to the single domain camelid nanobody vhh T4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VL2
- Type
- protein
- Length
- 1,003 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T4 nanobody
- Ligands
- 9EG
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F, G, H | T4 nanobody | protein | 125 | 5% helix, 50% strand | — |
| B, C, D | T4 nanobody | protein | 126 | 5% helix, 50% strand | — |
Ligands and binding sites
- 9EG · N-(4-chlorophenyl)-N'-(3,4-dichlorophenyl)urea · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.79 | 0.81 | 88 | empty |
| 2 | 973 | 0.72 | 0.76 | 87 | empty |
| 3 | 77 | 0.61 | 0.90 | 22 | 9EG |
| 4 | 82 | 0.61 | 0.89 | 24 | 9EG |
| 5 | 81 | 0.60 | 0.88 | 22 | 9EG |
Interfaces
13 interfaces between chains.
- A–C · 673 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 661 Ų buried · 11 hydrogen bonds · protein-protein
- F–H · 636 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 609 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 327 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5VL2 · The hapten triclocarban bound to the single domain camelid nanobody VHH T4 · 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 5VL2 · PDBe 5VL2
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