Research workbench
SARS-cov-2 spike in complex with neutralizing Fab 2B04 (one up, two down conformation)
Analyse SARS-cov-2 spike in complex with neutralizing Fab 2B04 (one up, two down… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K9H
- Type
- protein
- Length
- 3,391 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 2B04 heavy chain; 2B04 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, FUC, MAN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 950 | 25% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 994 | 23% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 991 | 24% helix, 31% strand | P0DTC2 |
| H, I | 2B04 heavy chain | protein | 119 | 3% helix, 49% strand | — |
| L, M | 2B04 light chain | protein | 109 | 0% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 82 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 17 copies · chains C
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · 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 | 773 | 0.85 | 0.88 | 78 | empty |
| 2 | 980 | 0.83 | 0.84 | 114 | empty |
| 3 | 1066 | 0.81 | 0.82 | 108 | empty |
| 4 | 706 | 0.80 | 0.84 | 70 | empty |
| 5 | 727 | 0.78 | 0.82 | 61 | empty |
Interfaces
12 interfaces between chains.
- A–B · 4423 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 4342 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 4039 Ų buried · 31 hydrogen bonds · protein-protein
- H–L · 815 Ų buried · 1 hydrogen bond · protein-protein
- I–M · 680 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 7K9H · SARS-CoV-2 Spike in complex with neutralizing Fab 2B04 (one up, two down conformation) · 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 7K9H · PDBe 7K9H · UniProt P0DTC2
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