Research workbench
Structure of OC43 spike in complex with polyclonal FAB4 (donor 269)
Analyse Structure of OC43 spike in complex with polyclonal FAB4 (donor 269) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SBV
- Type
- protein
- Length
- 3,740 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein; Human polyclonal Fab model with polyalanine backbone - heavy chain
- UniProt
- A0A7U1BGV5
- Ligands
- 8Z9, NAG, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J | Spike protein | protein | 1176 | 21% helix, 31% strand | A0A7U1BGV5 |
| A | Spike protein | protein | 1172 | 22% helix, 33% strand | A0A7U1BGV5 |
| B | Spike protein | protein | 1183 | 21% helix, 33% strand | A0A7U1BGV5 |
| H | Human polyclonal Fab model with polyalanine backbone - heavy chain | protein | 113 | 3% helix, 41% strand | — |
| L | Human polyclonal Fab model with polyalanine backbone - heavy chain | protein | 96 | 3% helix, 26% strand | — |
Ligands and binding sites
- 8Z9 · Sapienic acid · ligand · 3 copies · chains J, A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 55 copies · chains J, A, B
- BMA · beta-D-mannopyranose · sugar
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 | 1102 | 0.86 | 0.87 | 125 | empty |
| 2 | 570 | 0.86 | 0.91 | 65 | empty |
| 3 | 847 | 0.84 | 0.86 | 99 | empty |
| 4 | 212 | 0.84 | 0.96 | 31 | 8Z9 |
| 5 | 219 | 0.84 | 0.96 | 29 | 8Z9 |
Interfaces
6 interfaces between chains.
- J–A · 5923 Ų buried · 66 hydrogen bonds · protein-protein
- J–B · 5894 Ų buried · 69 hydrogen bonds · protein-protein
- A–B · 5823 Ų buried · 64 hydrogen bonds · protein-protein
- H–L · 323 Ų buried · 0 hydrogen bonds · protein-protein
- J–H · 222 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 63 disulfide, 39 glycan (disulfide, N-glycosylation).
Compared structures
- 7SBV · Structure of OC43 spike in complex with polyclonal Fab4 (Donor 269) · the same entry in another collection · chain J against J, 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 A0A7U1BGV5
- Elsewhere: RCSB PDB 7SBV · PDBe 7SBV · UniProt A0A7U1BGV5
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