Research workbench
Structural basis for inhibition of erythrocyte invasion by antibodies to plasmodium falciparum protein cyrpa
Analyse Structural basis for inhibition of erythrocyte invasion by antibodies to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TIH
- Type
- protein
- Length
- 750 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine-rich protective antigen; Cyrpa antibody Fab heavy chain; Cyrpa antibody Fab…
- UniProt
- Q8IFM8
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine-rich protective antigen | protein | 326 | 1% helix, 55% strand | Q8IFM8 |
| H | Cyrpa antibody Fab heavy chain | protein | 212 | 8% helix, 51% strand | — |
| L | Cyrpa antibody Fab light chain | protein | 212 | 6% helix, 51% strand | — |
Ligands and binding sites
- ACT · Acetate ion · additive · 3 copies · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 765 | 0.77 | 0.81 | 77 | ACT |
| 2 | 86 | 0.59 | 0.88 | 28 | empty |
| 3 | 189 | 0.46 | 0.75 | 32 | empty |
| 4 | 84 | 0.37 | 0.77 | 17 | empty |
| 5 | 75 | 0.36 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1737 Ų buried · 13 hydrogen bonds · protein-protein
- A–H · 650 Ų buried · 17 hydrogen bonds · protein-protein
- A–L · 372 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 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 0.99
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 5TIH · PDBe 5TIH · UniProt Q8IFM8
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