Research workbench
Cryo-EM structure of the omicron S in complex with 35B5 FAB(1 down- and 2 up rbds)
Analyse Cryo-EM structure of the omicron S in complex with 35B5 FAB(1 down- and 2 up… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WLY
- Type
- protein
- Length
- 3,627 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain of 35B5 Fab; Light chain of 35B5 Fab
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 21% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1051 | 23% helix, 27% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1042 | 22% helix, 25% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1058 | 21% helix, 26% strand | P0DTC2 |
| P, Y | Heavy chain of 35B5 Fab | protein | 127 | 0% helix, 37% strand | — |
| O, X | Light chain of 35B5 Fab | protein | 111 | 0% helix, 42% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 31 copies · chains A, C, B
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 | 1074 | 0.85 | 0.86 | 126 | empty |
| 2 | 801 | 0.84 | 0.87 | 103 | empty |
| 3 | 622 | 0.84 | 0.88 | 48 | empty |
| 4 | 985 | 0.83 | 0.84 | 106 | empty |
| 5 | 628 | 0.82 | 0.87 | 75 | empty |
Interfaces
11 interfaces between chains.
- A–C · 5669 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 4660 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 4580 Ų buried · 40 hydrogen bonds · protein-protein
- C–Y · 1065 Ų buried · 14 hydrogen bonds · protein-protein
- B–P · 1046 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 43 disulfide, 29 glycan (disulfide, N-glycosylation).
Compared structures
- 7WLY · Cryo-EM structure of the Omicron S in complex with 35B5 Fab(1 down- and 2 up RBDs) · 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 7WLY · PDBe 7WLY · UniProt P0DTC2
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