Research workbench
PFS48/45 central and C-terminal domains bound to Fab fragments of monoclonal antibody 10D8 and 32F3
Analyse PFS48/45 central and C-terminal domains bound to Fab fragments of monoclonal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZWM
- Type
- protein
- Length
- 2,179 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gametocyte surface protein P45/48; 32F3 heavy chain; 32F3 light chain; 10D8 heavy chain…
- UniProt
- Q8I6T1
- Ligands
- NAG, BMA, FUC
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 9 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gametocyte surface protein P45/48 | protein | 237 | 5% helix, 49% strand | Q8I6T1 |
| B | 32F3 heavy chain | protein | 213 | 7% helix, 50% strand | — |
| C, H | 32F3 light chain | protein | 211 | 6% helix, 51% strand | — |
| D | 10D8 heavy chain | protein | 213 | 7% helix, 49% strand | — |
| E | 10D8 light chain | protein | 217 | 5% helix, 49% strand | — |
| F | Gametocyte surface protein P45/48 | protein | 230 | 4% helix, 50% strand | Q8I6T1 |
| G | 32F3 heavy chain | protein | 216 | 9% helix, 49% strand | — |
| I | 10D8 heavy chain | protein | 215 | 7% helix, 48% strand | — |
| J | 10D8 light chain | protein | 216 | 5% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, E, F, J
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains E, J
- FUC · alpha-L-fucopyranose · sugar · chains 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.71 | 0.81 | 60 | empty |
| 2 | 319 | 0.70 | 0.84 | 33 | empty |
| 3 | 581 | 0.70 | 0.79 | 63 | empty |
| 4 | 246 | 0.67 | 0.84 | 31 | empty |
| 5 | 275 | 0.64 | 0.81 | 42 | empty |
Interfaces
15 interfaces between chains.
- D–E · 2005 Ų buried · 22 hydrogen bonds · protein-protein
- I–J · 1945 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1869 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1869 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 1054 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7ZWM · Pfs48/45 central and C-terminal domains bound to Fab fragments of monoclonal antibody… · the same entry in another collection · chain J against J, TM-score 1.00
- Q8I6T1 · AlphaFold monomer V2.0 prediction for gametocyte surface protein P45/48 (Q8I6T1) · a predicted model of the same protein · chain F against A, TM-score 0.91
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 Q8I6T1
- Elsewhere: RCSB PDB 7ZWM · PDBe 7ZWM · UniProt Q8I6T1
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