Research workbench
Beta-32 Fab in complex with SARS-cov-2 beta-spike glycoprotein
Analyse Beta-32 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
- 7Q9K
- Type
- protein
- Length
- 3,388 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Beta-32 heavy chain; Beta-32 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 943 | 24% helix, 33% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1002 | 22% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 979 | 23% helix, 32% strand | P0DTC2 |
| H, D | Beta-32 heavy chain | protein | 125 | 10% helix, 46% strand | — |
| L, E | Beta-32 light chain | protein | 107 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 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 | 1082 | 0.87 | 0.88 | 141 | empty |
| 2 | 589 | 0.83 | 0.88 | 83 | empty |
| 3 | 468 | 0.77 | 0.85 | 42 | empty |
| 4 | 539 | 0.75 | 0.83 | 42 | empty |
| 5 | 503 | 0.75 | 0.83 | 42 | empty |
Interfaces
8 interfaces between chains.
- A–C · 4369 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 4364 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 4305 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 1022 Ų buried · 8 hydrogen bonds · protein-protein
- H–L · 1013 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 41 disulfide (N-glycosylation, disulfide).
Compared structures
- 7Q9K · Beta-32 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 7Q9K · PDBe 7Q9K · UniProt P0DTC2
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