Research workbench
Ceratotoxin variant in complex with specific antibody Fab fragment
Analyse Ceratotoxin variant in complex with specific antibody Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EPM
- Type
- protein
- Length
- 940 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab fragment heavy chain; Antibody Fab fragment light chain…
- UniProt
- P84507
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Antibody Fab fragment heavy chain | protein | 219 | 10% helix, 52% strand | — |
| B, F | Antibody Fab fragment light chain | protein | 218 | 6% helix, 52% strand | — |
| C, D | Beta-theraphotoxin-CM1A | protein | 33 | 9% helix, 30% strand | P84507 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.70 | 0.75 | 72 | empty |
| 2 | 579 | 0.62 | 0.74 | 67 | empty |
| 3 | 114 | 0.57 | 0.84 | 20 | empty |
| 4 | 239 | 0.54 | 0.77 | 32 | empty |
| 5 | 263 | 0.54 | 0.76 | 46 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1922 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1880 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 542 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 453 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 357 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 5EPM · Ceratotoxin variant in complex with specific antibody Fab fragment · the same entry in another collection · chain C against C, TM-score 1.00
- P84507 · AlphaFold monomer V2.0 prediction for beta-theraphotoxin-CM1A (P84507) · a predicted model of the same protein · chain C against A, TM-score 0.90
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 P84507
- Elsewhere: RCSB PDB 5EPM · PDBe 5EPM · UniProt P84507
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