MolNFT v1 · #168741 · protein
Structure of the SARS-cov-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment (open state)
6WPT: “Structure of the SARS-cov-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment…”. Electron microscopy, 4 ligands (NAG, BMA, FUC). MolNFT v1 #168741 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6WPT
- Type
- protein
- Length
- 3,277 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, FUC, MAN
Structure
electron microscopy · 6 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 945 | — | P0DTC2 |
| B | — | protein | 937 | — | P0DTC2 |
| C | — | protein | 952 | — | P0DTC2 |
| H, D | — | protein | 123 | — | — |
| L | — | protein | 99 | — | — |
| E | — | protein | 98 | — | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 59 copies · chains A, E, B, C, L
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains D, E, H, L
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 6WPT · Structure of the SARS-CoV-2 spike glycoprotein in complex with the S309 neutralizing… · 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 P0DTC2
- Elsewhere: RCSB PDB 6WPT · PDBe 6WPT · UniProt P0DTC2
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