Research workbench
S protein of SARS-cov-2 in complex with 2G1
Analyse S protein of SARS-cov-2 in complex with 2G1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7X08
- Type
- protein
- Length
- 4,572 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain of 2G1; Light chain of 2G1
- UniProt
- P0DTC2
- Ligands
- EIC, NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 15% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1099 | 20% helix, 33% strand | P0DTC2 |
| H, I, J | Heavy chain of 2G1 | protein | 214 | 3% helix, 48% strand | — |
| L, M, N | Light chain of 2G1 | protein | 211 | 5% helix, 38% strand | — |
Ligands and binding sites
- EIC · Linoleic acid · ligand · 3 copies · chains A, C, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 78 copies · chains A, B, C, J, H
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 | 1083 | 0.83 | 0.84 | 129 | empty |
| 2 | 376 | 0.82 | 0.91 | 51 | empty |
| 3 | 425 | 0.82 | 0.90 | 67 | EIC |
| 4 | 883 | 0.82 | 0.84 | 112 | empty |
| 5 | 378 | 0.82 | 0.91 | 50 | empty |
Interfaces
17 interfaces between chains.
- A–B · 6620 Ų buried · 54 hydrogen bonds · protein-protein
- A–C · 6555 Ų buried · 53 hydrogen bonds · protein-protein
- B–C · 6532 Ų buried · 49 hydrogen bonds · protein-protein
- I–M · 1855 Ų buried · 8 hydrogen bonds · protein-protein
- J–N · 1849 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 disulfide, 54 glycan (disulfide, N-glycosylation).
Compared structures
- 7X08 · S protein of SARS-CoV-2 in complex with 2G1 · 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 7X08 · PDBe 7X08 · UniProt P0DTC2
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