Research workbench
Structure of the membrane soluble spike complex from the lassa virus in a C1-symmetric MAP focused on the ectodomain
Analyse Structure of the membrane soluble spike complex from the lassa virus in a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PVD
- Type
- protein
- Length
- 1,035 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
- 18 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a, b, c | Glycoprotein G2 | protein | 160 | 41% helix, 16% strand | P08669 |
| A, B, C | Pre-glycoprotein polyprotein gp complex | protein | 185 | 25% helix, 24% strand | P08669 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, a, B, b, C, c
- XYS · alpha-D-xylopyranose · sugar · 7 copies · chains B, A, C
- BDP · beta-D-glucopyranuronic acid · sugar · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.83 | 0.91 | 44 | empty |
| 2 | 561 | 0.75 | 0.82 | 83 | empty |
| 3 | 154 | 0.74 | 0.92 | 28 | empty |
| 4 | 206 | 0.69 | 0.87 | 35 | empty |
| 5 | 144 | 0.68 | 0.89 | 27 | empty |
Interfaces
12 interfaces between chains.
- c–C · 2441 Ų buried · 25 hydrogen bonds · protein-protein
- b–B · 2406 Ų buried · 21 hydrogen bonds · protein-protein
- a–A · 2366 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1181 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1152 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 glycan, 18 disulfide (N-glycosylation, disulfide).
Compared structures
- 7PVD · Structure of the membrane soluble spike complex from the Lassa virus in a C1-symmetric… · the same entry in another collection · chain b against b, 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 7PVD · PDBe 7PVD · UniProt P08669
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