MolNFT v1 · #40846 · protein
Structure of a plasmodium falciparum apical membrane antigen 1-Fab F8. 12.19 complex
2J5L: “Structure of a plasmodium falciparum apical membrane antigen 1-Fab F8. 12.19 complex”. X-ray diffraction, 8 pockets (best druggability 0.63). MolNFT v1 #40846 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2J5L
- 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
- Q9GVB7
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apical membrane antigen 1 | protein | 34 | 9% helix, 21% strand | Q9GVB7 |
| B | Fab fragment of monoclonal antibody F8.12.19 | protein | 213 | 6% helix, 50% strand | — |
| C | Fab fragment of monoclonal antibody F8.12.19 | protein | 225 | 8% helix, 46% strand | — |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.63 | 0.74 | 67 | empty |
| 2 | 134 | 0.52 | 0.81 | 27 | empty |
| 3 | 59 | 0.47 | 0.85 | 21 | empty |
| 4 | 123 | 0.47 | 0.79 | 25 | empty |
| 5 | 74 | 0.40 | 0.79 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2023 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 561 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 297 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 2J5L · Structure of a Plasmodium falciparum apical membrane antigen 1-Fab F8. 12.19 complex · the same entry in another collection · chain A against A, 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 Q9GVB7
- Elsewhere: RCSB PDB 2J5L · PDBe 2J5L · UniProt Q9GVB7
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