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Structure of the SARS-cov-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, C104
Analyse Structure of the SARS-cov-2 S 6P trimer in complex with the human neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K8U
- Type
- protein
- Length
- 3,181 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; C104 Fab heavy chain; C104 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- 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 | 991 | 22% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 986 | 23% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 991 | 23% helix, 30% strand | P0DTC2 |
| H | C104 Fab heavy chain | protein | 106 | 8% helix, 45% strand | — |
| L | C104 Fab light chain | protein | 107 | 3% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A, C
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 | 1059 | 0.85 | 0.86 | 123 | empty |
| 2 | 648 | 0.82 | 0.87 | 91 | empty |
| 3 | 322 | 0.80 | 0.90 | 49 | empty |
| 4 | 717 | 0.79 | 0.84 | 67 | empty |
| 5 | 634 | 0.76 | 0.83 | 89 | empty |
Interfaces
7 interfaces between chains.
- A–B · 4392 Ų buried · 55 hydrogen bonds · protein-protein
- B–C · 4031 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 4030 Ų buried · 33 hydrogen bonds · protein-protein
- A–H · 258 Ų buried · 0 hydrogen bonds · protein-protein
- B–L · 245 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7K8U · Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody… · 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 7K8U · PDBe 7K8U · UniProt P0DTC2
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