Research workbench
Pfcyrpa bound to monoclonal antibody CY.004 Fab fragment
Analyse Pfcyrpa bound to monoclonal antibody CY.004 Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PHW
- Type
- protein
- Length
- 1,494 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine-rich protective antigen; Monoclonal antibody CY.004 heavy chain; Monoclonal…
- UniProt
- Q8IFM8
- Ligands
- CA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine-rich protective antigen | protein | 317 | 1% helix, 55% strand | Q8IFM8 |
| B | Monoclonal antibody CY.004 heavy chain | protein | 223 | 5% helix, 52% strand | — |
| C | Monoclonal antibody CY.004 light chain | protein | 209 | 7% helix, 52% strand | — |
| D | Cysteine-rich protective antigen | protein | 312 | 4% helix, 59% strand | Q8IFM8 |
| E | Monoclonal antibody CY.004 heavy chain | protein | 226 | 5% helix, 51% strand | — |
| F | Monoclonal antibody CY.004 light chain | protein | 207 | 7% helix, 52% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 905 | 0.77 | 0.80 | 76 | empty |
| 2 | 836 | 0.77 | 0.80 | 68 | empty |
| 3 | 384 | 0.58 | 0.75 | 41 | empty |
| 4 | 253 | 0.56 | 0.77 | 37 | empty |
| 5 | 313 | 0.54 | 0.75 | 47 | empty |
Interfaces
8 interfaces between chains.
- B–C · 1945 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1891 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 562 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 541 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 294 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 7PHW · PfCyRPA bound to monoclonal antibody Cy.004 Fab fragment · the same entry in another collection · chain F against F, 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 0.98
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 7PHW · PDBe 7PHW · UniProt Q8IFM8
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