Research workbench
SARS-cov-2 omicron variant S trimer complexed with three JMB2002 Fab
Analyse SARS-cov-2 omicron variant S trimer complexed with three JMB2002 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WPF
- Type
- protein
- Length
- 4,743 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; JMB2002 Fab heavy chain; JMB2002 Fab light chain; Anti-Fab nanobody
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1024 | 22% helix, 32% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1023 | 22% helix, 33% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1022 | 23% helix, 32% strand | P0DTC2 |
| R, U, X | JMB2002 Fab heavy chain | protein | 225 | 4% helix, 50% strand | — |
| S, V, Y | JMB2002 Fab light chain | protein | 213 | 8% helix, 46% strand | — |
| T, W, Z | Anti-Fab nanobody | protein | 120 | 3% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 copies · chains A, B, C
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 | 1025 | 0.85 | 0.86 | 117 | empty |
| 2 | 737 | 0.83 | 0.87 | 98 | empty |
| 3 | 632 | 0.83 | 0.88 | 46 | empty |
| 4 | 543 | 0.77 | 0.84 | 50 | empty |
| 5 | 309 | 0.77 | 0.88 | 49 | empty |
Interfaces
15 interfaces between chains.
- A–C · 4601 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 4078 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 3730 Ų buried · 26 hydrogen bonds · protein-protein
- U–V · 1617 Ų buried · 4 hydrogen bonds · protein-protein
- X–Y · 1426 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 disulfide, 36 glycan (disulfide, N-glycosylation).
Compared structures
- 7WPF · SARS-CoV-2 Omicron Variant S Trimer complexed with three JMB2002 Fab · 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 7WPF · PDBe 7WPF · UniProt P0DTC2
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