Research workbench
Structure of the SARS-CoV-2 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-3
Analyse Structure of the SARS-CoV-2 S 6P trimer in complex with the mouse antibody Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UZ4
- Type
- protein
- Length
- 3,867 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Mus musculus; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein; M8a-3 Fab heavy chain; M8a-3 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 3.1 · 3 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1063 | 22% helix, 31% strand | P0DTC2 |
| H, M, P | M8a-3 Fab heavy chain | protein | 120 | 5% helix, 47% strand | — |
| L, N, Q | M8a-3 Fab light chain | protein | 106 | 0% helix, 39% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 51 copies · chains A, B, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.84 | 0.87 | 97 | empty |
| 2 | 1142 | 0.83 | 0.84 | 131 | empty |
| 3 | 527 | 0.80 | 0.87 | 48 | empty |
| 4 | 588 | 0.76 | 0.82 | 44 | empty |
| 5 | 216 | 0.75 | 0.90 | 37 | empty |
Interfaces
12 interfaces between chains.
- A–B · 4305 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 4267 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 4070 Ų buried · 38 hydrogen bonds · protein-protein
- M–N · 976 Ų buried · 6 hydrogen bonds · protein-protein
- H–L · 960 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 42 disulfide (N-glycosylation, disulfide).
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 7UZ4 · PDBe 7UZ4 · UniProt P0DTC2
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