MolNFT v1 · #123576 · protein
Crystal structure of anti-glycan antibody FAB14.22 in complex with streptococcus pneumoniae serotype 14 tetrasaccharide at 1.75 a
5JOP · Fab 14.22 light chain: “Crystal structure of anti-glycan antibody FAB14.22 in complex with streptococcus pneumoniae serotype 14…”. X-ray diffraction, 4 ligands (GAL, NAG, BGC), 9 pockets (best druggability 0.83). MolNFT v1 #123576…
- PDB
- 5JOP
- Type
- protein
- Length
- 855 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 14.22 light chain; FAB14.22 heavy chain
- Ligands
- GAL, NAG, BGC, PO4
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, L | Fab 14.22 light chain | protein | 218 | 5% helix, 52% strand | — |
| E | FAB14.22 heavy chain | protein | 208 | 10% helix, 55% strand | — |
| H | FAB14.22 heavy chain | protein | 211 | 9% helix, 56% strand | — |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains D, E, L, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E, H
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains D, E, L, H
- PO4 · Phosphate ion · ion · 6 copies · chains E, L, H
- GOL · Glycerol · additive · 16 copies · chains D, E, L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.83 | 0.84 | 117 | GOL |
| 2 | 137 | 0.71 | 0.91 | 28 | empty |
| 3 | 155 | 0.54 | 0.80 | 20 | NAG, GAL |
| 4 | 91 | 0.52 | 0.84 | 20 | empty |
| 5 | 120 | 0.49 | 0.79 | 19 | GAL |
Interfaces
6 interfaces between chains.
- L–H · 1838 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1730 Ų buried · 16 hydrogen bonds · protein-protein
- E–L · 551 Ų buried · 4 hydrogen bonds · protein-protein
- E–H · 349 Ų buried · 8 hydrogen bonds · protein-protein
- D–L · 332 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 covalent (disulfide, additive adduct).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5JOP · PDBe 5JOP
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