Research workbench
Structure of the Fab fragment of N62, a protective monoclonal antibody to the nonreducing end of francisella tularensis O-antigen
Analyse Structure of the Fab fragment of N62, a protective monoclonal antibody to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KPH
- Type
- protein
- Length
- 810 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N62 light chain; N62 heavy chain
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | N62 light chain | protein | 210 | 6% helix, 51% strand | — |
| H | N62 heavy chain | protein | 206 | 6% helix, 55% strand | — |
| M | N62 light chain | protein | 196 | 4% helix, 51% strand | — |
| I | N62 heavy chain | protein | 198 | 5% helix, 57% strand | — |
Ligands and binding sites
- ACT · Acetate ion · additive · chains M, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.71 | 0.76 | 88 | empty |
| 2 | 290 | 0.62 | 0.80 | 44 | empty |
| 3 | 203 | 0.59 | 0.81 | 26 | empty |
| 4 | 159 | 0.59 | 0.83 | 33 | empty |
| 5 | 52 | 0.41 | 0.82 | 12 | empty |
Interfaces
5 interfaces between chains.
- M–I · 1752 Ų buried · 17 hydrogen bonds · protein-protein
- L–H · 1744 Ų buried · 15 hydrogen bonds · protein-protein
- L–I · 227 Ų buried · 6 hydrogen bonds · protein-protein
- H–I · 79 Ų buried · 1 hydrogen bond · protein-protein
- H–M · 47 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 modified (disulfide, cyclization, oxidation).
Compared structures
- 4KPH · Structure of the Fab fragment of N62, a protective monoclonal antibody to the nonreducing… · the same entry in another collection · chain L against L, 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 4KPH · PDBe 4KPH
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.