MolNFT v1 · #179378 · protein
An ultra-potent human neutralizing antibody locks the SARS-cov-2 spike in the closed conformation
7K3Q · Fab fragment of S2E12 monoclonal antibody, heavy chain: “An ultra-potent human neutralizing antibody locks the SARS-cov-2 spike in the closed conformation”. X-ray diffraction, 5 pockets (best druggability 0.63). MolNFT v1 #179378 on…
- PDB
- 7K3Q
- Type
- protein
- Length
- 442 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab fragment of S2E12 monoclonal antibody, heavy chain; Fab fragment of S2E12 monoclonal…
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab fragment of S2E12 monoclonal antibody, heavy chain | protein | 226 | 11% helix, 50% strand | — |
| L | Fab fragment of S2E12 monoclonal antibody, light chain | protein | 216 | 7% helix, 53% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.63 | 0.75 | 53 | empty |
| 2 | 74 | 0.58 | 0.89 | 21 | empty |
| 3 | 72 | 0.36 | 0.77 | 21 | empty |
| 4 | 75 | 0.32 | 0.74 | 16 | EDO |
| 5 | 63 | 0.27 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- H–L · 1992 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7K3Q · An ultra-potent human neutralizing antibody locks the SARS-CoV-2 spike in the closed… · 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
- Elsewhere: RCSB PDB 7K3Q · PDBe 7K3Q
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