MolNFT v1 · #188924 · protein
Crystal structure of malaria transmission-blocking antigen PFS48/45-6C variant in complex with human antibodies rupa-117 and rupa-47
7UNB · Rupa-47 Fab kappa chain: “Crystal structure of malaria transmission-blocking antigen PFS48/45-6C variant in complex with human…”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.71). MolNFT v1 #188924 on GenesisL1…
- PDB
- 7UNB
- Type
- protein
- Length
- 1,017 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rupa-47 Fab kappa chain; Gametocyte surface protein P45/48; Rupa-117 Fab kappa chain…
- UniProt
- Q8I6T1
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Rupa-47 Fab kappa chain | protein | 214 | 7% helix, 50% strand | — |
| R | Gametocyte surface protein P45/48 | protein | 138 | 8% helix, 54% strand | Q8I6T1 |
| E | Rupa-117 Fab kappa chain | protein | 214 | 6% helix, 51% strand | — |
| H | Rupa-47 Fab heavy chain | protein | 221 | 11% helix, 52% strand | — |
| F | Rupa-117 Fab heavy chain | protein | 230 | 8% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.71 | 0.81 | 72 | empty |
| 2 | 665 | 0.64 | 0.74 | 65 | empty |
| 3 | 184 | 0.55 | 0.79 | 20 | empty |
| 4 | 311 | 0.54 | 0.75 | 39 | empty |
| 5 | 120 | 0.40 | 0.75 | 22 | empty |
Interfaces
8 interfaces between chains.
- E–F · 2043 Ų buried · 24 hydrogen bonds · protein-protein
- L–H · 1708 Ų buried · 15 hydrogen bonds · protein-protein
- R–H · 616 Ų buried · 12 hydrogen bonds · protein-protein
- R–F · 544 Ų buried · 13 hydrogen bonds · protein-protein
- L–R · 503 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7UNB · Crystal structure of malaria transmission-blocking antigen Pfs48/45-6C variant in complex… · the same entry in another collection · chain L against L, 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 R against A, TM-score 0.95
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 7UNB · PDBe 7UNB · UniProt Q8I6T1
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