Research workbench
Crystal structure of the engineered neutralizing antibody M18 complexed with anthrax protective antigen domain 4
Analyse Crystal structure of the engineered neutralizing antibody M18 complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ETB
- Type
- protein
- Length
- 1,485 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4…
- UniProt
- P13423
- Pockets
- 18 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, I | Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker | protein | 227 | 3% helix, 33% strand | — |
| G, H | Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker | protein | 228 | 3% helix, 30% strand | — |
| J, K, M | Anthrax protective antigen | protein | 144 | 13% helix, 22% strand | P13423 |
| L | Anthrax protective antigen | protein | 143 | 11% helix, 22% strand | P13423 |
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.68 | 0.79 | 38 | empty |
| 2 | 417 | 0.64 | 0.78 | 34 | empty |
| 3 | 395 | 0.63 | 0.78 | 36 | empty |
| 4 | 390 | 0.63 | 0.78 | 35 | empty |
| 5 | 507 | 0.62 | 0.75 | 50 | empty |
Interfaces
12 interfaces between chains.
- I–M · 928 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 927 Ų buried · 12 hydrogen bonds · protein-protein
- G–K · 924 Ų buried · 15 hydrogen bonds · protein-protein
- F–J · 922 Ų buried · 14 hydrogen bonds · protein-protein
- H–I · 546 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3ETB · Crystal structure of the engineered neutralizing antibody M18 complexed with anthrax… · the same entry in another collection · chain M against M, TM-score 1.00
- P13423 · AlphaFold monomer V2.0 prediction for protective antigen (P13423) · a predicted model of the same protein · chain L against A, TM-score 0.98
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 P13423
- Elsewhere: RCSB PDB 3ETB · PDBe 3ETB · UniProt P13423
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