Research workbench
BD23-Fab in complex with the S ectodomain trimer
Analyse BD23-Fab in complex with the S ectodomain trimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BYR
- Type
- protein
- Length
- 3,137 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; AB23-Fab-heavy chain; AB23-Fab-light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 959 | 23% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 998 | 22% helix, 29% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 973 | 21% helix, 31% strand | P0DTC2 |
| H | AB23-Fab-heavy chain | protein | 102 | 0% helix, 32% strand | — |
| L | AB23-Fab-light chain | protein | 105 | 3% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 44 copies · chains A, B, C, H
- BMA · beta-D-mannopyranose · sugar · chains H
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 | 835 | 0.82 | 0.85 | 99 | empty |
| 2 | 852 | 0.80 | 0.83 | 86 | empty |
| 3 | 439 | 0.77 | 0.86 | 48 | empty |
| 4 | 489 | 0.76 | 0.84 | 40 | empty |
| 5 | 281 | 0.75 | 0.88 | 55 | empty |
Interfaces
6 interfaces between chains.
- B–C · 5334 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 4877 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 4538 Ų buried · 37 hydrogen bonds · protein-protein
- H–L · 856 Ų buried · 10 hydrogen bonds · protein-protein
- B–H · 785 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 disulfide, 38 glycan (disulfide, N-glycosylation).
Compared structures
- 7BYR · BD23-Fab in complex with the S ectodomain trimer · 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 7BYR · PDBe 7BYR · UniProt P0DTC2
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