Research workbench
Cryo-EM structure of S309-rbd-rbd-S309 in the S309-bound omicron spike protein (local refinement)
Analyse Cryo-EM structure of S309-rbd-rbd-S309 in the S309-bound omicron spike protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7YAD
- Type
- protein
- Length
- 848 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S309 neutralizing antibody heavy chain; S309 neutralizing antibody light chain; Spike…
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 11 · best druggability 0.65
Structure
electron microscopy · 6 distinct chains · 8% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S309 neutralizing antibody heavy chain | protein | 124 | 5% helix, 47% strand | — |
| B | S309 neutralizing antibody light chain | protein | 105 | 0% helix, 50% strand | — |
| M | Spike protein S1 | protein | 200 | 17% helix, 26% strand | P0DTC2 |
| C | S309 neutralizing antibody heavy chain | protein | 126 | 2% helix, 47% strand | — |
| D | S309 neutralizing antibody light chain | protein | 108 | 3% helix, 48% strand | — |
| E | Spike protein S1 | protein | 185 | 14% helix, 26% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, M, C, D, E
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.65 | 0.78 | 57 | NAG, FUC |
| 2 | 342 | 0.55 | 0.75 | 31 | empty |
| 3 | 270 | 0.53 | 0.75 | 35 | NAG |
| 4 | 134 | 0.44 | 0.77 | 21 | empty |
| 5 | 129 | 0.44 | 0.77 | 19 | empty |
Interfaces
7 interfaces between chains.
- A–B · 739 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 734 Ų buried · 4 hydrogen bonds · protein-protein
- A–M · 696 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 679 Ų buried · 8 hydrogen bonds · protein-protein
- M–E · 360 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7YAD · Cryo-EM structure of S309-RBD-RBD-S309 in the S309-bound Omicron spike protein (local… · 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 7YAD · PDBe 7YAD · UniProt P0DTC2
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