MolNFT v1 · #160050 · protein
Structure of lassa virus glycoprotein in complex with Fab 25.6A
6P95 · Pre-glycoprotein polyprotein gp complex: “Structure of lassa virus glycoprotein in complex with Fab 25.6A”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.87). MolNFT v1 #160050 on GenesisL1: 3D…
- PDB
- 6P95
- Type
- protein
- Length
- 2,299 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-glycoprotein polyprotein gp complex; Fab antibody heavy chain; Fab antibody light…
- UniProt
- P08669
- Ligands
- NAG, BMA, MAN, FUC
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 10 distinct chains · 21% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pre-glycoprotein polyprotein gp complex | protein | 188 | 26% helix, 26% strand | P08669 |
| B | Pre-glycoprotein polyprotein gp complex | protein | 181 | 27% helix, 28% strand | P08669 |
| C | Pre-glycoprotein polyprotein gp complex | protein | 189 | 25% helix, 26% strand | P08669 |
| D, F | Fab antibody heavy chain | protein | 218 | 5% helix, 51% strand | — |
| E | Fab antibody light chain | protein | 212 | 6% helix, 49% strand | — |
| G, L | Fab antibody light chain | protein | 212 | 6% helix, 49% strand | — |
| H | Fab antibody heavy chain | protein | 219 | 5% helix, 50% strand | — |
| a | Pre-glycoprotein polyprotein gp complex | protein | 153 | 45% helix, 14% strand | P08669 |
| b | Pre-glycoprotein polyprotein gp complex | protein | 145 | 48% helix, 15% strand | P08669 |
| c | Pre-glycoprotein polyprotein gp complex | protein | 152 | 48% helix, 14% strand | P08669 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 47 copies · chains A, a, B, b, C, c, E, G, L
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains L, a, E, b, G, c, A, B, C
- MAN · alpha-D-mannopyranose · sugar · 7 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.87 | 0.88 | 103 | empty |
| 2 | 376 | 0.75 | 0.86 | 50 | empty |
| 3 | 429 | 0.75 | 0.85 | 44 | empty |
| 4 | 704 | 0.74 | 0.79 | 54 | empty |
| 5 | 728 | 0.71 | 0.78 | 60 | empty |
Interfaces
33 interfaces between chains.
- A–a · 2481 Ų buried · 25 hydrogen bonds · protein-protein
- B–b · 2429 Ų buried · 24 hydrogen bonds · protein-protein
- C–c · 2413 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1743 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1714 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide, 28 glycan (disulfide, N-glycosylation).
Compared structures
- 6P95 · Structure of Lassa virus glycoprotein in complex with Fab 25.6A · the same entry in another collection · chain G against G, 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 6P95 · PDBe 6P95 · UniProt P08669
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