Research workbench
Pfcyrpa bound to monoclonal antibody CY.007 Fab fragment
Analyse Pfcyrpa bound to monoclonal antibody CY.007 Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PHV
- Type
- protein
- Length
- 1,476 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine-rich protective antigen; Monoclonal antibody CY.007 heavy chain; Monoclonal…
- UniProt
- Q8IFM8
- Ligands
- NH4
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 3% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine-rich protective antigen | protein | 316 | 0% helix, 56% strand | Q8IFM8 |
| B | Monoclonal antibody CY.007 heavy chain | protein | 221 | 5% helix, 49% strand | — |
| C, F | Monoclonal antibody CY.007 light chain | protein | 207 | 6% helix, 43% strand | — |
| D | Cysteine-rich protective antigen | protein | 305 | 0% helix, 56% strand | Q8IFM8 |
| E | Monoclonal antibody CY.007 heavy chain | protein | 220 | 5% helix, 54% strand | — |
Ligands and binding sites
- NH4 · Ammonium ion · ion · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.78 | 0.80 | 73 | empty |
| 2 | 925 | 0.78 | 0.80 | 68 | empty |
| 3 | 480 | 0.62 | 0.76 | 53 | empty |
| 4 | 345 | 0.60 | 0.77 | 45 | empty |
| 5 | 471 | 0.60 | 0.75 | 62 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1923 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1918 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 596 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 585 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 263 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 7PHV · PfCyRPA bound to monoclonal antibody Cy.007 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 D 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 7PHV · PDBe 7PHV · UniProt Q8IFM8
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