MolNFT v1 · #169460 · protein
Structure of the SARS-cov-2 spike glycoprotein in complex with the C105 neutralizing antibody Fab fragment (state 2)
6XCN: “Structure of the SARS-cov-2 spike glycoprotein in complex with the C105 neutralizing antibody Fab fragment…”. Electron microscopy, 3 ligands (NAG, BMA, FUC), 20 pockets (best druggability 0.86). MolNFT v1 #169460 on GenesisL1: 3D…
- PDB
- 6XCN
- Type
- protein
- Length
- 3,636 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; C105 Fab heavy chain; C105 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, FUC
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 19% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Spike glycoprotein | protein | 985 | 23% helix, 28% strand | P0DTC2 |
| B, F, H | C105 Fab heavy chain | protein | 116 | 3% helix, 28% strand | — |
| D, G, L | C105 Fab light chain | protein | 111 | 0% helix, 37% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 54 copies · chains A, C, E
- BMA · beta-D-mannopyranose · sugar · 3 copies
- FUC · alpha-L-fucopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.86 | 0.88 | 95 | empty |
| 2 | 600 | 0.83 | 0.88 | 53 | empty |
| 3 | 859 | 0.82 | 0.84 | 86 | empty |
| 4 | 547 | 0.73 | 0.81 | 37 | empty |
| 5 | 501 | 0.73 | 0.81 | 37 | empty |
Interfaces
12 interfaces between chains.
- A–E · 4283 Ų buried · 31 hydrogen bonds · protein-protein
- C–E · 4264 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 4256 Ų buried · 31 hydrogen bonds · protein-protein
- F–G · 758 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 755 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide, 42 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 6XCN · Structure of the SARS-CoV-2 spike glycoprotein in complex with the C105 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 6XCN · PDBe 6XCN · UniProt P0DTC2
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