Research workbench
SARS-COV2 omicron varient S protein structure in complex with neutralizing monoclonal antibody 002-S21F2
Analyse SARS-COV2 omicron varient S protein structure in complex with neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UPL
- Type
- protein
- Length
- 4,031 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Mab 002-S21F2 light chain; Mab 002-S21F2 heavy chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 19% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Spike glycoprotein | protein | 1050 | 22% helix, 29% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1053 | 23% helix, 27% strand | P0DTC2 |
| D, I | Mab 002-S21F2 light chain | protein | 215 | 5% helix, 47% strand | — |
| E, F | Mab 002-S21F2 heavy chain | protein | 224 | 1% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 54 copies · chains A, C, B, F
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 | 974 | 0.86 | 0.87 | 117 | empty |
| 2 | 958 | 0.85 | 0.86 | 101 | empty |
| 3 | 719 | 0.85 | 0.88 | 63 | empty |
| 4 | 682 | 0.85 | 0.89 | 79 | empty |
| 5 | 772 | 0.84 | 0.87 | 78 | empty |
Interfaces
10 interfaces between chains.
- A–C · 5262 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 5085 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 4864 Ų buried · 24 hydrogen bonds · protein-protein
- F–I · 1658 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 1499 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 48 disulfide, 42 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 7UPL · SARS-Cov2 Omicron varient S protein structure in complex with neutralizing monoclonal… · 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 7UPL · PDBe 7UPL · UniProt P0DTC2
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