Research workbench
Locally refined region of SARS-cov-2 spike in complex with IgG 553-60
Analyse Locally refined region of SARS-cov-2 spike in complex with IgG 553-60 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WOC
- Type
- protein
- Length
- 610 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; MAB60 vh; MAB60 vl
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.52
Structure
electron microscopy · 3 distinct chains · 4% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Spike protein S1 | protein | 194 | 7% helix, 28% strand | P0DTC2 |
| A | MAB60 vh | protein | 204 | 1% helix, 39% strand | — |
| B | MAB60 vl | protein | 212 | 4% helix, 31% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.52 | 0.73 | 44 | empty |
| 2 | 163 | 0.45 | 0.75 | 25 | empty |
| 3 | 80 | 0.33 | 0.74 | 22 | empty |
| 4 | 79 | 0.32 | 0.74 | 19 | empty |
| 5 | 58 | 0.32 | 0.77 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1674 Ų buried · 11 hydrogen bonds · protein-protein
- C–A · 618 Ų buried · 4 hydrogen bonds · protein-protein
- C–B · 111 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7WOC · Locally refined region of SARS-CoV-2 Spike in complex with IgG 553-60 · the same entry in another collection · chain C against C, 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 7WOC · PDBe 7WOC · UniProt P0DTC2
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