MolNFT v1 · #137324 · protein
The hapten triclocarban bound to the single domain camelid nanobody vhh T4
5VL2 · T4 nanobody: “The hapten triclocarban bound to the single domain camelid nanobody vhh T4”. X-ray diffraction, 1 ligand (9EG), 15 pockets (best druggability 0.79). MolNFT v1 #137324 on GenesisL1: 3D structure, binding sites and…
- 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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