Research workbench
Beta-26 Fab in complex with SARS-cov-2 beta-spike glycoprotein
Analyse Beta-26 Fab in complex with SARS-cov-2 beta-spike glycoprotein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q9J
- Type
- protein
- Length
- 3,794 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Beta-26 light chain; Beta-26 heavy chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1037 | 22% helix, 35% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1034 | 22% helix, 35% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1033 | 23% helix, 35% strand | P0DTC2 |
| L, F, K | Beta-26 light chain | protein | 108 | 6% helix, 48% strand | — |
| H, E, J | Beta-26 heavy chain | protein | 122 | 5% helix, 55% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 57 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.84 | 0.89 | 79 | empty |
| 2 | 458 | 0.79 | 0.87 | 54 | empty |
| 3 | 341 | 0.76 | 0.87 | 60 | empty |
| 4 | 391 | 0.76 | 0.86 | 46 | empty |
| 5 | 486 | 0.76 | 0.84 | 44 | empty |
Interfaces
13 interfaces between chains.
- B–C · 4223 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 4204 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 4099 Ų buried · 32 hydrogen bonds · protein-protein
- L–H · 876 Ų buried · 8 hydrogen bonds · protein-protein
- J–K · 872 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide, 44 glycan (disulfide, N-glycosylation).
Compared structures
- 7Q9J · Beta-26 fab in complex with SARS-CoV-2 beta-Spike glycoprotein · 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 7Q9J · PDBe 7Q9J · UniProt P0DTC2
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