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Structural basis for antibody-mediated neutralization of lassa virus
Analyse Structural basis for antibody-mediated neutralization of lassa virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VK2
- Type
- protein
- Length
- 2,313 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-glycoprotein polyprotein gp complex; Fab 37.7H heavy chain; Fab 37.7H light chain
- UniProt
- P08669
- Ligands
- NAG, BMA, MAN, FUC
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 10 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-glycoprotein polyprotein gp complex | protein | 186 | 28% helix, 24% strand | P08669 |
| a | Pre-glycoprotein polyprotein gp complex | protein | 155 | 44% helix, 13% strand | P08669 |
| B, C | Pre-glycoprotein polyprotein gp complex | protein | 185 | 27% helix, 24% strand | P08669 |
| b | Pre-glycoprotein polyprotein gp complex | protein | 159 | 42% helix, 13% strand | P08669 |
| c | Pre-glycoprotein polyprotein gp complex | protein | 157 | 42% helix, 13% strand | P08669 |
| D | Fab 37.7H heavy chain | protein | 218 | 6% helix, 54% strand | — |
| E, G | Fab 37.7H light chain | protein | 211 | 6% helix, 50% strand | — |
| F | Fab 37.7H heavy chain | protein | 217 | 6% helix, 55% strand | — |
| H | Fab 37.7H heavy chain | protein | 217 | 6% helix, 54% strand | — |
| L | Fab 37.7H light chain | protein | 212 | 6% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 51 copies · chains A, a, L, B, b, G, C, c, E
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains a, E, A, B, c, G, C
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains a, b, c
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.83 | 0.94 | 43 | empty |
| 2 | 540 | 0.79 | 0.86 | 64 | empty |
| 3 | 498 | 0.79 | 0.86 | 66 | empty |
| 4 | 845 | 0.79 | 0.82 | 97 | empty |
| 5 | 689 | 0.73 | 0.79 | 54 | empty |
Interfaces
33 interfaces between chains.
- C–c · 2544 Ų buried · 30 hydrogen bonds · protein-protein
- A–a · 2538 Ų buried · 26 hydrogen bonds · protein-protein
- B–b · 2493 Ų buried · 23 hydrogen bonds · protein-protein
- F–G · 1716 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1710 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide, 31 glycan (disulfide, N-glycosylation).
Compared structures
- 5VK2 · Structural basis for antibody-mediated neutralization of Lassa virus · 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 P08669
- Elsewhere: RCSB PDB 5VK2 · PDBe 5VK2 · UniProt P08669
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