MolNFT v1 · #118361 · protein
Crystal structure of Fab of parasite invasion inhibitory antibody C1 - hexagonal form
5EZI · Fab C12 heavy chain: “Crystal structure of Fab of parasite invasion inhibitory antibody C1 - hexagonal form”. X-ray diffraction, 6 ligands (NAG, MAN, BMA), 4 pockets (best druggability 0.60). MolNFT v1 #118361 on GenesisL1: 3D…
- PDB
- 5EZI
- Type
- protein
- Length
- 436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab C12 heavy chain; Fab C12 light chain
- Ligands
- NAG, MAN, BMA, GAL, FUC, CL
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab C12 heavy chain | protein | 222 | 7% helix, 51% strand | — |
| L | Fab C12 light chain | protein | 214 | 6% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains H
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- GAL · beta-D-galactopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains H
- CL · Chloride ion · ion · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.60 | 0.74 | 58 | empty |
| 2 | 74 | 0.31 | 0.74 | 19 | empty |
| 3 | 79 | 0.31 | 0.74 | 21 | CL |
| 4 | 73 | 0.30 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- H–L · 1935 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5EZI · Crystal Structure of Fab of parasite invasion inhibitory antibody c1 - hexagonal form · the same entry in another collection · chain H against H, 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 5EZI · PDBe 5EZI
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