Research workbench
B6 Fab fragment bound to the HKU4 spike stem helix peptide
Analyse B6 Fab fragment bound to the HKU4 spike stem helix peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M52
- Type
- protein
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein stem helix peptide; B6 antigen-binding (Fab) fragment heavy chain; B6…
- UniProt
- A3EX94
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein stem helix peptide | protein | 11 | 73% helix, 0% strand | A3EX94 |
| H | B6 antigen-binding (Fab) fragment heavy chain | protein | 220 | 8% helix, 52% strand | — |
| L | B6 antigen-binding (Fab) fragment light chain | protein | 218 | 6% helix, 52% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.59 | 0.92 | 20 | GOL |
| 2 | 394 | 0.55 | 0.74 | 50 | empty |
| 3 | 122 | 0.40 | 0.75 | 24 | empty |
| 4 | 117 | 0.39 | 0.75 | 26 | GOL |
Interfaces
3 interfaces between chains.
- H–L · 1960 Ų buried · 25 hydrogen bonds · protein-protein
- A–H · 445 Ų buried · 4 hydrogen bonds · protein-protein
- A–L · 223 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7M52 · B6 Fab fragment bound to the HKU4 spike stem helix peptide · 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 A3EX94
- Elsewhere: RCSB PDB 7M52 · PDBe 7M52 · UniProt A3EX94
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