MolNFT v1 · #118362 · protein
Crystal structure of Fab of parasite invasion inhibitory antibody C1 - orthorhombic form
5EZJ · Fab C12 heavy chain: “Crystal structure of Fab of parasite invasion inhibitory antibody C1 - orthorhombic form”. X-ray diffraction, 3 ligands (NAG, BMA, FUC), 7 pockets (best druggability 0.59). MolNFT v1 #118362 on GenesisL1: 3D…
- PDB
- 5EZJ
- Type
- protein
- Length
- 435 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, BMA, FUC
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab C12 heavy chain | protein | 222 | 8% helix, 51% strand | — |
| B | Fab C12 light chain | protein | 213 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.59 | 0.75 | 48 | empty |
| 2 | 51 | 0.44 | 0.84 | 21 | empty |
| 3 | 88 | 0.38 | 0.76 | 15 | empty |
| 4 | 60 | 0.32 | 0.76 | 14 | empty |
| 5 | 75 | 0.30 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1836 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5EZJ · Crystal Structure of Fab of parasite invasion inhibitory antibody c1 - orthorhombic form · the same entry in another collection · chain A against A, 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 5EZJ · PDBe 5EZJ
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