Research workbench
B6 Fab fragment bound to the OC43 spike stem helix peptide
Analyse B6 Fab fragment bound to the OC43 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
- 7M51
- Type
- protein
- Length
- 448 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
- P36334
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein stem helix peptide | protein | 11 | 82% helix, 0% strand | P36334 |
| H | B6 antigen-binding (Fab) fragment heavy chain | protein | 219 | 8% helix, 50% strand | — |
| L | B6 antigen-binding (Fab) fragment light chain | protein | 218 | 6% helix, 53% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 4 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 | 381 | 0.55 | 0.74 | 50 | empty |
| 2 | 51 | 0.55 | 0.90 | 21 | GOL |
| 3 | 159 | 0.44 | 0.75 | 25 | empty |
| 4 | 149 | 0.42 | 0.75 | 28 | GOL |
Interfaces
3 interfaces between chains.
- H–L · 1983 Ų buried · 24 hydrogen bonds · protein-protein
- A–H · 453 Ų buried · 4 hydrogen bonds · protein-protein
- A–L · 242 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7M51 · B6 Fab fragment bound to the OC43 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 P36334
- Elsewhere: RCSB PDB 7M51 · PDBe 7M51 · UniProt P36334
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.