Research workbench
Pfcyrpa bound to monoclonal antibody CY.003 Fab fragment
Analyse Pfcyrpa bound to monoclonal antibody CY.003 Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PI2
- Type
- protein
- Length
- 3,002 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine-rich protective antigen; Monoclonal antibody CY.003 heavy chain; Monoclonal…
- UniProt
- Q8IFM8
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 9 distinct chains · 4% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine-rich protective antigen | protein | 321 | 0% helix, 54% strand | Q8IFM8 |
| B | Monoclonal antibody CY.003 heavy chain | protein | 222 | 9% helix, 51% strand | — |
| C, I | Monoclonal antibody CY.003 light chain | protein | 208 | 6% helix, 52% strand | — |
| D | Cysteine-rich protective antigen | protein | 327 | 1% helix, 54% strand | Q8IFM8 |
| E | Monoclonal antibody CY.003 heavy chain | protein | 223 | 9% helix, 48% strand | — |
| F, L | Monoclonal antibody CY.003 light chain | protein | 207 | 5% helix, 53% strand | — |
| G | Cysteine-rich protective antigen | protein | 310 | 0% helix, 56% strand | Q8IFM8 |
| H, K | Monoclonal antibody CY.003 heavy chain | protein | 225 | 8% helix, 50% strand | — |
| J | Cysteine-rich protective antigen | protein | 319 | 0% helix, 53% strand | Q8IFM8 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 698 | 0.80 | 0.85 | 119 | empty |
| 2 | 776 | 0.80 | 0.83 | 91 | empty |
| 3 | 1157 | 0.78 | 0.80 | 93 | empty |
| 4 | 820 | 0.78 | 0.81 | 86 | empty |
| 5 | 930 | 0.78 | 0.80 | 86 | empty |
Interfaces
25 interfaces between chains.
- B–C · 1925 Ų buried · 20 hydrogen bonds · protein-protein
- H–I · 1887 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1827 Ų buried · 15 hydrogen bonds · protein-protein
- K–L · 1814 Ų buried · 20 hydrogen bonds · protein-protein
- J–K · 508 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide (disulfide).
Compared structures
- 7PI2 · PfCyRPA bound to monoclonal antibody Cy.003 Fab fragment · the same entry in another collection · chain L against L, 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
- Every structure of UniProt Q8IFM8
- Elsewhere: RCSB PDB 7PI2 · PDBe 7PI2 · UniProt Q8IFM8
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