Research workbench
SARS-cov-2 omicron variant spike protein with three XGV347 fabs binding to three closed state rbds
Analyse SARS-cov-2 omicron variant spike protein with three XGV347 fabs binding to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WEC
- Type
- protein
- Length
- 3,984 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- The heavy chain of Fab XGV347; The light chain of Fab XGV347; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, H, I | The heavy chain of Fab XGV347 | protein | 123 | 2% helix, 46% strand | — |
| J, K, L | The light chain of Fab XGV347 | protein | 107 | 0% helix, 41% strand | — |
| A, B, C | Spike glycoprotein | protein | 1098 | 20% helix, 28% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 73 copies · chains A, B, C, G, I, H
- BMA · beta-D-mannopyranose · sugar · 5 copies
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 | 884 | 0.89 | 0.91 | 98 | empty |
| 2 | 962 | 0.83 | 0.85 | 115 | empty |
| 3 | 749 | 0.82 | 0.86 | 96 | empty |
| 4 | 548 | 0.81 | 0.87 | 60 | empty |
| 5 | 549 | 0.81 | 0.87 | 70 | empty |
Interfaces
15 interfaces between chains.
- A–C · 5395 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 5383 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 5372 Ų buried · 24 hydrogen bonds · protein-protein
- I–K · 825 Ų buried · 4 hydrogen bonds · protein-protein
- G–J · 786 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 glycan, 48 disulfide (disulfide, N-glycosylation, glycosylation, C-mannosylation).
Compared structures
- 7WEC · SARS-CoV-2 Omicron variant spike protein with three XGv347 Fabs binding to three closed… · the same entry in another collection · chain G against G, 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 7WEC · PDBe 7WEC · UniProt P0DTC2
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