Research workbench
SARS-cov-2 spike in complex with neutralizing Fab 2H04 (three down conformation)
Analyse SARS-cov-2 spike in complex with neutralizing Fab 2H04 (three down conformation) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K9J
- Type
- protein
- Length
- 3,627 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 2H04 heavy chain; 2H04 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, FUC, MAN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 19% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 982 | 23% helix, 32% strand | P0DTC2 |
| H, I, J | 2H04 heavy chain | protein | 121 | 5% helix, 48% strand | — |
| L, M, N | 2H04 light chain | protein | 106 | 3% helix, 41% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 84 copies · chains A, C, H, B, I, J
- BMA · beta-D-mannopyranose · sugar · 18 copies · chains C, H, A, I, B, J
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains H, L, A, I, M, B, J, N, 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 | 673 | 0.85 | 0.89 | 74 | empty |
| 2 | 558 | 0.82 | 0.88 | 73 | empty |
| 3 | 520 | 0.80 | 0.87 | 64 | empty |
| 4 | 459 | 0.79 | 0.87 | 49 | empty |
| 5 | 441 | 0.79 | 0.87 | 52 | empty |
Interfaces
12 interfaces between chains.
- A–B · 4975 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 4970 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 4941 Ų buried · 38 hydrogen bonds · protein-protein
- J–N · 862 Ų buried · 7 hydrogen bonds · protein-protein
- I–M · 855 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 7K9J · SARS-CoV-2 Spike in complex with neutralizing Fab 2H04 (three 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 7K9J · PDBe 7K9J · UniProt P0DTC2
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