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Ternary complex among two human derived single chain antibody fragments and CN2 toxin from scorpion centruroides noxius.
Analyse Ternary complex among two human derived single chain antibody fragments and CN2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4V1D
- Type
- protein
- Length
- 525 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single chain antibody fragment lr, heavy chain; Single chain antibody fragment lr, light…
- UniProt
- P01495
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single chain antibody fragment lr, heavy chain | protein | 117 | 10% helix, 54% strand | — |
| B | Single chain antibody fragment lr, light chain | protein | 108 | 3% helix, 49% strand | — |
| C | Beta-mammal toxin CN2 | protein | 65 | 17% helix, 28% strand | P01495 |
| D | Single chain antibody fragment RU1, heavy chain | protein | 124 | 5% helix, 51% strand | — |
| E | Single chain antibody fragment RU1, light chain | protein | 111 | 3% helix, 49% strand | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.61 | 0.77 | 44 | empty |
| 2 | 178 | 0.54 | 0.79 | 24 | empty |
| 3 | 100 | 0.39 | 0.76 | 24 | empty |
| 4 | 59 | 0.30 | 0.75 | 14 | empty |
Interfaces
6 interfaces between chains.
- D–E · 845 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 745 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 688 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 687 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 324 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 4V1D · Ternary complex among two human derived single chain antibody fragments and Cn2 toxin… · the same entry in another collection · chain A against A, TM-score 1.00
- P01495 · AlphaFold monomer V2.0 prediction for beta-mammal toxin CN2 (P01495) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P01495
- Elsewhere: RCSB PDB 4V1D · PDBe 4V1D · UniProt P01495
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