Research workbench
Beta-43 Fab in complex with SARS-cov-2 beta-spike glycoprotein
Analyse Beta-43 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
- 7Q9I
- Type
- protein
- Length
- 3,881 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Beta-43 heavy chain; Beta-43 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1062 | 22% helix, 35% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1058 | 23% helix, 34% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1059 | 22% helix, 35% strand | P0DTC2 |
| H, E, J | Beta-43 heavy chain | protein | 126 | 5% helix, 48% strand | — |
| L, F, K | Beta-43 light chain | protein | 108 | 6% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 53 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 | 1107 | 0.87 | 0.88 | 123 | empty |
| 2 | 865 | 0.86 | 0.88 | 103 | empty |
| 3 | 904 | 0.82 | 0.84 | 77 | empty |
| 4 | 865 | 0.81 | 0.84 | 86 | empty |
| 5 | 646 | 0.74 | 0.81 | 56 | empty |
Interfaces
12 interfaces between chains.
- A–B · 4203 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 4182 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 3697 Ų buried · 20 hydrogen bonds · protein-protein
- J–K · 984 Ų buried · 11 hydrogen bonds · protein-protein
- H–L · 984 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide, 41 glycan (disulfide, N-glycosylation).
Compared structures
- 7Q9I · Beta-43 fab in complex with SARS-CoV-2 beta-Spike glycoprotein · the same entry in another collection · chain B against B, 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 7Q9I · PDBe 7Q9I · UniProt P0DTC2
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