Research workbench
Cryo-EM structure of NTD-directed neutralizing antibody 2-17 Fab in complex with SARS-CoV-2 S2P spike
Analyse Cryo-EM structure of NTD-directed neutralizing antibody 2-17 Fab in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LQW
- Type
- protein
- Length
- 3,374 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.47
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- 2-17 Heavy Chain; 2-17 Light Chain; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 4.47 · 5 distinct chains · 19% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 2-17 Heavy Chain | protein | 124 | 0% helix, 36% strand | — |
| L | 2-17 Light Chain | protein | 109 | 0% helix, 45% strand | — |
| B | Spike glycoprotein | protein | 1038 | 22% helix, 28% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1066 | 19% helix, 23% strand | P0DTC2 |
| A | Spike glycoprotein | protein | 1037 | 20% helix, 27% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 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 | 947 | 0.87 | 0.88 | 113 | empty |
| 2 | 628 | 0.85 | 0.90 | 80 | empty |
| 3 | 1195 | 0.83 | 0.84 | 176 | empty |
| 4 | 494 | 0.82 | 0.88 | 60 | empty |
| 5 | 666 | 0.80 | 0.85 | 85 | empty |
Interfaces
6 interfaces between chains.
- B–A · 6034 Ų buried · 56 hydrogen bonds · protein-protein
- C–A · 5129 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 5090 Ų buried · 42 hydrogen bonds · protein-protein
- H–L · 434 Ų buried · 0 hydrogen bonds · protein-protein
- H–C · 267 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 7LQW · Cryo-EM structure of ntd-directed neutralizing antibody 2-17 Fab in complex with… · 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 7LQW · PDBe 7LQW · UniProt P0DTC2
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