Research workbench
CC6.33 IgG in complex with SARS-cov-2-6P-MUT7 S protein (non-uniform refinement)
Analyse CC6.33 IgG in complex with SARS-cov-2-6P-MUT7 S protein (non-uniform refinement) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RU3
- Type
- protein
- Length
- 3,537 residues
- Chains
- 7
- 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
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, E | CC6.33 IgG heavy chain fv | protein | 116 | 5% helix, 52% strand | — |
| L, F | CC6.33 IgG kappa chain fv | protein | 107 | 6% helix, 49% strand | — |
| A | Spike glycoprotein | protein | 1062 | 22% helix, 35% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 989 | 22% helix, 33% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1040 | 23% helix, 33% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 41 copies · chains H, L, A, B, E, F, C
- FUC · alpha-L-fucopyranose · sugar · chains B, E
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 | 1092 | 0.87 | 0.88 | 129 | empty |
| 2 | 1177 | 0.86 | 0.87 | 102 | empty |
| 3 | 816 | 0.83 | 0.86 | 98 | empty |
| 4 | 865 | 0.79 | 0.82 | 92 | empty |
| 5 | 752 | 0.78 | 0.82 | 84 | empty |
Interfaces
10 interfaces between chains.
- A–B · 5158 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 4707 Ų buried · 49 hydrogen bonds · protein-protein
- C–B · 4322 Ų buried · 41 hydrogen bonds · protein-protein
- H–L · 698 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 684 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 disulfide, 35 glycan (disulfide, N-glycosylation).
Compared structures
- 7RU3 · CC6.33 IgG in complex with SARS-CoV-2-6P-Mut7 S protein (non-uniform 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 7RU3 · PDBe 7RU3 · UniProt P0DTC2
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