Research workbench
SARS-cov-2 spike in complex with the S2M11 neutralizing antibody Fab fragment
Analyse SARS-cov-2 spike in complex with the S2M11 neutralizing antibody Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K43
- Type
- protein
- Length
- 3,783 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; S2M11 Fab fragment (heavy chain); S2M11 Fab fragment (light chain)
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, FUC
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 20% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Spike glycoprotein | protein | 1034 | 23% helix, 34% strand | P0DTC2 |
| H, C, F | S2M11 Fab fragment (heavy chain) | protein | 122 | 12% helix, 48% strand | — |
| L, D, G | S2M11 Fab fragment (light chain) | protein | 105 | 6% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 72 copies · chains A, G, B, L, E, D
- BMA · beta-D-mannopyranose · sugar · 3 copies
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, F, H, B, C, E
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 | 1040 | 0.88 | 0.89 | 140 | empty |
| 2 | 807 | 0.84 | 0.87 | 109 | empty |
| 3 | 1019 | 0.83 | 0.84 | 91 | empty |
| 4 | 1007 | 0.83 | 0.84 | 98 | empty |
| 5 | 870 | 0.83 | 0.85 | 72 | empty |
Interfaces
18 interfaces between chains.
- A–B · 5028 Ų buried · 49 hydrogen bonds · protein-protein
- B–E · 5025 Ų buried · 49 hydrogen bonds · protein-protein
- A–E · 5023 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 816 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 815 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 glycan, 48 disulfide (N-glycosylation, disulfide).
Compared structures
- 7K43 · SARS-CoV-2 spike in complex with the S2M11 neutralizing antibody Fab fragment · 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 7K43 · PDBe 7K43 · UniProt P0DTC2
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