Research workbench
Structure of the SARS-cov-2 S1 subunit in complex with antibody N-612- 004
Analyse Structure of the SARS-cov-2 S1 subunit in complex with antibody N-612- 004 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S0E
- Type
- protein
- Length
- 1,076 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; N-612-004 Fab heavy chain; N-612-004 light chain
- UniProt
- P0DTC2
- Pockets
- 13 · best druggability 0.72
Structure
electron microscopy · 3 distinct chains · 6% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 639 | 7% helix, 34% strand | P0DTC2 |
| H | N-612-004 Fab heavy chain | protein | 223 | 1% helix, 31% strand | — |
| L | N-612-004 light chain | protein | 214 | 7% helix, 38% strand | — |
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.72 | 0.79 | 76 | empty |
| 2 | 191 | 0.64 | 0.84 | 30 | empty |
| 3 | 203 | 0.61 | 0.82 | 26 | empty |
| 4 | 538 | 0.60 | 0.74 | 60 | empty |
| 5 | 86 | 0.57 | 0.86 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1823 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 396 Ų buried · 5 hydrogen bonds · protein-protein
- A–L · 309 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 7S0E · Structure of the SARS-CoV-2 S1 subunit in complex with antibody N-612-004 · 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 7S0E · PDBe 7S0E · UniProt P0DTC2
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