Research workbench
J08 fragment antigen binding in complex with SARS-cov-2-6P-MUT2 S protein (conformation 2)
Analyse J08 fragment antigen binding in complex with SARS-cov-2-6P-MUT2 S protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S6K
- Type
- protein
- Length
- 3,885 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; J08 fragment antigen binding heavy chain variable domain; J08…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Spike glycoprotein | protein | 1070 | 20% helix, 35% strand | P0DTC2 |
| H, C, F | J08 fragment antigen binding heavy chain variable domain | protein | 122 | 8% helix, 43% strand | — |
| L, D, G | J08 fragment antigen binding light chain variable domain | protein | 103 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 45 copies · chains A, 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 | 872 | 0.84 | 0.86 | 93 | empty |
| 2 | 450 | 0.83 | 0.90 | 58 | empty |
| 3 | 1005 | 0.79 | 0.81 | 84 | empty |
| 4 | 1042 | 0.78 | 0.80 | 97 | empty |
| 5 | 1188 | 0.77 | 0.79 | 92 | empty |
Interfaces
18 interfaces between chains.
- B–E · 4254 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 4252 Ų buried · 41 hydrogen bonds · protein-protein
- A–E · 4251 Ų buried · 41 hydrogen bonds · protein-protein
- H–L · 812 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 812 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 33 glycan (disulfide, N-glycosylation).
Compared structures
- 7S6K · J08 fragment antigen binding in complex with SARS-CoV-2-6P-Mut2 S protein (conformation 2) · 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 7S6K · PDBe 7S6K · UniProt P0DTC2
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