MolNFT v1 · #147212 · protein
Crystal structure of malaria transmission-blocking antigen PFS48/45 6C in complex with antibody 85RF45.1
6E62 · PF48/45: “Crystal structure of malaria transmission-blocking antigen PFS48/45 6C in complex with antibody 85RF45.1”. X-ray diffraction, 1 ligand (NAG), 12 pockets (best druggability 0.62). MolNFT v1 #147212 on GenesisL1: 3D…
- PDB
- 6E62
- Type
- protein
- Length
- 1,134 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PF48/45; 85RF45.1 Fab heavy chain; 85RF45.1 Fab light chain
- UniProt
- A8QVT1
- Ligands
- NAG
- Pockets
- 12 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P, A | PF48/45 | protein | 137 | 6% helix, 50% strand | A8QVT1 |
| H, B | 85RF45.1 Fab heavy chain | protein | 217 | 6% helix, 57% strand | — |
| L, C | 85RF45.1 Fab light chain | protein | 213 | 6% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains P, A
- GOL · Glycerol · additive · 2 copies · chains P, H, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 474 | 0.62 | 0.76 | 60 | empty |
| 2 | 224 | 0.52 | 0.77 | 33 | empty |
| 3 | 249 | 0.51 | 0.75 | 29 | empty |
| 4 | 156 | 0.50 | 0.78 | 23 | empty |
| 5 | 85 | 0.47 | 0.82 | 16 | empty |
Interfaces
10 interfaces between chains.
- H–L · 1943 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1912 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 744 Ų buried · 15 hydrogen bonds · protein-protein
- P–H · 730 Ų buried · 13 hydrogen bonds · protein-protein
- P–L · 449 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6E62 · Crystal structure of malaria transmission-blocking antigen Pfs48/45 6C in complex with… · the same entry in another collection · chain P against P, 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 A8QVT1
- Elsewhere: RCSB PDB 6E62 · PDBe 6E62 · UniProt A8QVT1
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