Research workbench
CC6.33 IgG in complex with SARS-cov-2-6P-MUT7 S protein (RBD/FV local refinement)
Analyse CC6.33 IgG in complex with SARS-cov-2-6P-MUT7 S protein (RBD/FV local… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RU4
- Type
- protein
- Length
- 428 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CC6.33 IgG heavy chain fv; CC6.33 IgG kappa chain fv; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 6 · best druggability 0.64
Structure
electron microscopy · 3 distinct chains · 11% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | CC6.33 IgG heavy chain fv | protein | 118 | 5% helix, 53% strand | — |
| L | CC6.33 IgG kappa chain fv | protein | 108 | 6% helix, 50% strand | — |
| A | Spike glycoprotein | protein | 202 | 18% helix, 26% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains H, L, A
- FUC · alpha-L-fucopyranose · sugar · chains H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.64 | 0.85 | 38 | empty |
| 2 | 272 | 0.51 | 0.75 | 38 | NAG, FUC |
| 3 | 68 | 0.37 | 0.78 | 14 | empty |
| 4 | 72 | 0.34 | 0.76 | 20 | empty |
| 5 | 80 | 0.32 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 753 Ų buried · 6 hydrogen bonds · protein-protein
- H–A · 626 Ų buried · 5 hydrogen bonds · protein-protein
- L–A · 187 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7RU4 · CC6.33 IgG in complex with SARS-CoV-2-6P-Mut7 S protein (RBD/Fv local refinement) · 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 7RU4 · PDBe 7RU4 · UniProt P0DTC2
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