Research workbench
Structure of OC43 spike in complex with polyclonal FAB1 (donor 269)
Analyse Structure of OC43 spike in complex with polyclonal FAB1 (donor 269) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SB3
- Type
- protein
- Length
- 3,756 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 0.85
Structure
electron microscopy · 5 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J | Spike protein | protein | 1183 | 23% helix, 32% strand | A0A7U1BGV5 |
| A | Spike protein | protein | 1178 | 22% helix, 34% strand | A0A7U1BGV5 |
| B | Spike protein | protein | 1182 | 23% helix, 32% strand | A0A7U1BGV5 |
| H | Human polyclonal Fab model with polyalanine backbone - heavy chain | protein | 111 | 0% helix, 40% strand | — |
| L | Human polyclonal Fab model with polyalanine backbone - heavy chain | protein | 102 | 6% helix, 25% 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 | 862 | 0.85 | 0.87 | 115 | empty |
| 2 | 263 | 0.85 | 0.96 | 35 | 8Z9 |
| 3 | 920 | 0.85 | 0.86 | 109 | empty |
| 4 | 239 | 0.84 | 0.95 | 30 | 8Z9 |
| 5 | 217 | 0.84 | 0.96 | 31 | 8Z9 |
Interfaces
6 interfaces between chains.
- J–B · 5972 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 5969 Ų buried · 60 hydrogen bonds · protein-protein
- J–A · 5851 Ų buried · 57 hydrogen bonds · protein-protein
- H–L · 315 Ų buried · 0 hydrogen bonds · protein-protein
- B–L · 262 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 63 disulfide, 41 glycan (disulfide, N-glycosylation).
Compared structures
- 7SB3 · Structure of OC43 spike in complex with polyclonal Fab1 (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 7SB3 · PDBe 7SB3 · UniProt A0A7U1BGV5
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