MolNFT v1 · #186728 · protein
S2P6 Fab fragment bound to the SARS-COV/SARS-cov-2 spike stem helix peptide
7RNJ · Monoclonal antibody S2P6 Fab light chain: “S2P6 Fab fragment bound to the SARS-COV/SARS-cov-2 spike stem helix peptide”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.62). MolNFT v1 #186728 on GenesisL1: 3D…
- PDB
- 7RNJ
- Type
- protein
- Length
- 422 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monoclonal antibody S2P6 Fab light chain; Monoclonal antibody S2P6 Fab heavy chain; Spike…
- UniProt
- P0DTC2
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Monoclonal antibody S2P6 Fab light chain | protein | 210 | 5% helix, 48% strand | — |
| H | Monoclonal antibody S2P6 Fab heavy chain | protein | 198 | 7% helix, 42% strand | — |
| B | Spike glycoprotein stem helix peptide | protein | 14 | 79% helix, 0% strand | P0DTC2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains L, H
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 | 291 | 0.62 | 0.80 | 39 | empty |
| 2 | 106 | 0.44 | 0.78 | 23 | empty |
| 3 | 173 | 0.42 | 0.73 | 31 | empty |
| 4 | 115 | 0.36 | 0.73 | 16 | empty |
| 5 | 113 | 0.36 | 0.73 | 22 | SO4 |
Interfaces
3 interfaces between chains.
- L–H · 1204 Ų buried · 9 hydrogen bonds · protein-protein
- H–B · 367 Ų buried · 4 hydrogen bonds · protein-protein
- L–B · 261 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7RNJ · S2P6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide · the same entry in another collection · chain L against L, 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 7RNJ · PDBe 7RNJ · UniProt P0DTC2
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