MolNFT v1 · #68694 · protein
Crystal structure of a llama antibody complexed with the C. botulinum neurotoxin serotype a catalytic domain
3K3Q · Llama AA1 vhh domain: “Crystal structure of a llama antibody complexed with the C. botulinum neurotoxin serotype a catalytic domain”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.71). MolNFT v1 #68694 on…
- PDB
- 3K3Q
- Type
- protein
- Length
- 540 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Llama AA1 vhh domain; Botulinum neurotoxin type a
- EC
- 3.4.24.69
- UniProt
- A5HZZ9
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Llama AA1 vhh domain | protein | 137 | 9% helix, 44% strand | — |
| B | Botulinum neurotoxin type a (EC 3.4.24.69) | protein | 238 | 22% helix, 26% strand | A5HZZ9 |
| C | Botulinum neurotoxin type a (EC 3.4.24.69) | protein | 165 | 46% helix, 12% strand | A5HZZ9 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.71 | 0.94 | 22 | empty |
| 2 | 498 | 0.69 | 0.79 | 48 | empty |
| 3 | 200 | 0.58 | 0.81 | 26 | empty |
| 4 | 78 | 0.31 | 0.74 | 19 | empty |
| 5 | 61 | 0.29 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–C · 3897 Ų buried · 55 hydrogen bonds · protein-protein
- A–C · 430 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 318 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3K3Q · Crystal Structure of a Llama Antibody complexed with the C. Botulinum Neurotoxin Serotype… · 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 A5HZZ9
- Elsewhere: RCSB PDB 3K3Q · PDBe 3K3Q · UniProt A5HZZ9
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