MolNFT v1 · #171874 · protein
Atomic model of andes virus glycoprotein spike tetramer generated by fitting into a tula virus reconstruction
6ZJM · Envelope POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE…: “Atomic model of andes virus glycoprotein spike tetramer generated by fitting into a tula virus reconstruction”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 20 pockets (best…
- PDB
- 6ZJM
- Type
- protein
- Length
- 3,479 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE…
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 3 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Envelope POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE polyprotein | protein | 452 | 14% helix, 43% strand | — |
| B, D, F, H | Envelope POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE polyprotein | protein | 417 | 5% helix, 54% strand | — |
| G | Envelope POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE POLYPROTEIN,ENVELOPE polyprotein | protein | 455 | 14% helix, 42% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains E, F, G, H, C, D, A, B
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains F, H, D, B
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains E, F, G, H, C, D, A, B
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 | 1070 | 0.80 | 0.82 | 76 | empty |
| 2 | 1011 | 0.75 | 0.78 | 103 | empty |
| 3 | 928 | 0.74 | 0.78 | 96 | empty |
| 4 | 725 | 0.70 | 0.77 | 84 | empty |
| 5 | 650 | 0.68 | 0.77 | 74 | empty |
Interfaces
12 interfaces between chains.
- G–H · 1586 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1581 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1581 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1578 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 1283 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 96 disulfide, 13 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 6ZJM · Atomic model of Andes virus glycoprotein spike tetramer generated by fitting into a Tula… · 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
- Elsewhere: RCSB PDB 6ZJM · PDBe 6ZJM
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