Research workbench
Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape
Analyse Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M7W
- Type
- protein
- Length
- 2,136 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.65
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Monoclonal antibody S2X259 Fab light chain; Monoclonal antibody S2X259 Fab heavy chain…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · resolution 2.65 · 8 distinct chains · 9% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, L | Monoclonal antibody S2X259 Fab light chain | protein | 216 | 7% helix, 50% strand | — |
| A | Monoclonal antibody S2X259 Fab heavy chain | protein | 221 | 8% helix, 55% strand | — |
| D, F | Monoclonal antibody S2H97 Fab light chain | protein | 215 | 7% helix, 50% strand | — |
| C | Monoclonal antibody S2H97 Fab heavy chain | protein | 217 | 7% helix, 53% strand | — |
| H | Monoclonal antibody S2X259 Fab heavy chain | protein | 219 | 5% helix, 53% strand | — |
| E | Monoclonal antibody S2H97 Fab heavy chain | protein | 222 | 9% helix, 53% strand | — |
| S | Spike protein S1 | protein | 197 | 17% helix, 29% strand | P0DTC2 |
| R | Spike protein S1 | protein | 198 | 14% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains S, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.68 | 0.75 | 77 | empty |
| 2 | 288 | 0.68 | 0.83 | 35 | empty |
| 3 | 345 | 0.67 | 0.81 | 43 | empty |
| 4 | 533 | 0.61 | 0.74 | 63 | empty |
| 5 | 510 | 0.61 | 0.74 | 56 | empty |
Interfaces
13 interfaces between chains.
- L–H · 1883 Ų buried · 13 hydrogen bonds · protein-protein
- D–C · 1868 Ų buried · 18 hydrogen bonds · protein-protein
- F–E · 1810 Ų buried · 20 hydrogen bonds · protein-protein
- B–A · 1809 Ų buried · 17 hydrogen bonds · protein-protein
- H–R · 718 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7M7W · Antibodies to the SARS-cov-2 receptor-binding domain that maximize breadth and resistance… · 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 7M7W · PDBe 7M7W · UniProt P0DTC2
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