Research workbench
Crystal structure of pfcyrpa in complex with an invasion-inhibitory antibody Fab.
Analyse Crystal structure of pfcyrpa in complex with an invasion-inhibitory antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EZO
- Type
- protein
- Length
- 756 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pfcyrpa; C12 Fab
- UniProt
- Q8IFM8
- Ligands
- NAG, FUC
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Pfcyrpa | protein | 222 | 5% helix, 51% strand | — |
| L | C12 Fab | protein | 213 | 6% helix, 53% strand | — |
| A | C12 Fab | protein | 321 | 1% helix, 54% strand | Q8IFM8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains H
- FUC · alpha-L-fucopyranose · sugar · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.78 | 0.81 | 69 | empty |
| 2 | 70 | 0.56 | 0.88 | 18 | empty |
| 3 | 354 | 0.54 | 0.74 | 43 | empty |
| 4 | 147 | 0.47 | 0.77 | 30 | empty |
| 5 | 117 | 0.45 | 0.78 | 26 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1903 Ų buried · 21 hydrogen bonds · protein-protein
- L–A · 565 Ų buried · 9 hydrogen bonds · protein-protein
- H–A · 465 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5EZO · Crystal Structure of PfCyRPA in complex with an invasion-inhibitory antibody Fab. · the same entry in another collection · chain H against H, TM-score 1.00
- Q8IFM8 · AlphaFold monomer V2.0 prediction for cysteine-rich protective antigen (Q8IFM8) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q8IFM8
- Elsewhere: RCSB PDB 5EZO · PDBe 5EZO · UniProt Q8IFM8
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