MolNFT v1 · #185426 · protein
Structure of the membrane soluble spike complex from the lassa virus in a C3-symmetric MAP
7PUY · Glycoprotein G2: “Structure of the membrane soluble spike complex from the lassa virus in a C3-symmetric MAP”. Electron microscopy, 3 ligands (NAG, XYS, BDP), 15 pockets (best druggability 0.85). MolNFT v1 #185426 on GenesisL1: 3D…
- PDB
- 7PUY
- Type
- protein
- Length
- 1,224 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein G2; Pre-glycoprotein polyprotein gp complex
- UniProt
- P08669
- Ligands
- NAG, XYS, BDP
- Pockets
- 15 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a, b, c | Glycoprotein G2 | protein | 189 | 49% helix, 13% strand | P08669 |
| A, B, C | Pre-glycoprotein polyprotein gp complex | protein | 219 | 33% helix, 20% strand | P08669 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 copies · chains A, a, B, b, C, c
- XYS · alpha-D-xylopyranose · sugar · 6 copies · chains A, B, C
- BDP · beta-D-glucopyranuronic acid · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.85 | 0.86 | 63 | empty |
| 2 | 388 | 0.84 | 0.92 | 38 | empty |
| 3 | 1027 | 0.81 | 0.82 | 128 | empty |
| 4 | 133 | 0.70 | 0.91 | 27 | empty |
| 5 | 89 | 0.69 | 0.92 | 20 | empty |
Interfaces
15 interfaces between chains.
- c–C · 2633 Ų buried · 28 hydrogen bonds · protein-protein
- b–B · 2617 Ų buried · 24 hydrogen bonds · protein-protein
- a–A · 2613 Ų buried · 25 hydrogen bonds · protein-protein
- a–C · 1272 Ų buried · 11 hydrogen bonds · protein-protein
- b–c · 1261 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 glycan, 18 disulfide (N-glycosylation, disulfide).
Compared structures
- 7PUY · Structure of the membrane soluble spike complex from the Lassa virus in a C3-symmetric map · 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 7PUY · PDBe 7PUY · UniProt P08669
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.