MolNFT v1 · #40823 · protein
Structure of a plasmodium vivax apical membrane antigen 1-Fab F8.12.19 complex
2J4W: “Structure of a plasmodium vivax apical membrane antigen 1-Fab F8.12.19 complex”. X-ray diffraction, 5 pockets (best druggability 0.67). MolNFT v1 #40823 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2J4W
- Type
- protein
- Length
- 472 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apical membrane antigen 1; Fab fragment of monoclonal antibody F8.12.19
- UniProt
- Q9TY14
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Apical membrane antigen 1 | protein | 34 | 12% helix, 32% strand | Q9TY14 |
| H | Fab fragment of monoclonal antibody F8.12.19 | protein | 225 | 8% helix, 47% strand | — |
| L | Fab fragment of monoclonal antibody F8.12.19 | protein | 213 | 6% helix, 51% strand | — |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 687 | 0.67 | 0.76 | 70 | empty |
| 2 | 229 | 0.60 | 0.80 | 41 | empty |
| 3 | 118 | 0.46 | 0.78 | 23 | empty |
| 4 | 76 | 0.41 | 0.79 | 17 | empty |
| 5 | 101 | 0.35 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2034 Ų buried · 20 hydrogen bonds · protein-protein
- D–H · 625 Ų buried · 11 hydrogen bonds · protein-protein
- D–L · 236 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 2J4W · Structure of a Plasmodium vivax apical membrane antigen 1-Fab F8.12.19 complex · the same entry in another collection · chain D against D, 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 Q9TY14
- Elsewhere: RCSB PDB 2J4W · PDBe 2J4W · UniProt Q9TY14
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