Research workbench
SARS-cov-2 S omicron spike B.1.1.529 - 3-P2G3 and 1-P5C3 fabs (global)
Analyse SARS-cov-2 S omicron spike B.1.1.529 - 3-P2G3 and 1-P5C3 fabs (global) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QTI
- Type
- protein
- Length
- 5,061 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P2G3 heavy chain; P2G3 light chain; P5C3 light chain; P5C3 heavy chain; Spike…
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 7 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, B, I | P2G3 heavy chain | protein | 228 | 5% helix, 46% strand | — |
| H, C, J | P2G3 light chain | protein | 214 | 6% helix, 48% strand | — |
| E | P5C3 light chain | protein | 215 | 5% helix, 45% strand | — |
| F | P5C3 heavy chain | protein | 221 | 5% helix, 50% strand | — |
| D | Spike GLYCOPROTEIN,ENVELOPE glycoprotein | protein | 1103 | 20% helix, 26% strand | P0DTC2 |
| K | Spike GLYCOPROTEIN,ENVELOPE glycoprotein | protein | 1096 | 20% helix, 26% strand | P0DTC2 |
| A | Spike GLYCOPROTEIN,ENVELOPE glycoprotein | protein | 1100 | 21% helix, 25% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 copies · chains D, A, K
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains D
- MAN · alpha-D-mannopyranose · sugar
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 | 1166 | 0.88 | 0.89 | 104 | empty |
| 2 | 1073 | 0.87 | 0.88 | 121 | empty |
| 3 | 995 | 0.85 | 0.86 | 98 | empty |
| 4 | 1122 | 0.85 | 0.86 | 103 | empty |
| 5 | 846 | 0.83 | 0.86 | 91 | empty |
Interfaces
18 interfaces between chains.
- D–A · 5917 Ų buried · 40 hydrogen bonds · protein-protein
- D–K · 5103 Ų buried · 33 hydrogen bonds · protein-protein
- K–A · 4449 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 2065 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 2048 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 62 disulfide, 43 glycan (disulfide, N-glycosylation).
Compared structures
- 7QTI · SARS-CoV-2 S Omicron Spike B.1.1.529 - 3-P2G3 and 1-P5C3 Fabs (Global) · the same entry in another collection · chain H against H, 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 7QTI · PDBe 7QTI · UniProt P0DTC2
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