Research workbench
Ly-COV488 neutralizing antibody against SARS-cov-2
Analyse Ly-COV488 neutralizing antibody against SARS-cov-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KMH
- Type
- protein
- Length
- 616 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ly-COV488 Fab heavy chain; Ly-COV488 Fab light chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- PRO, NAG
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ly-COV488 Fab heavy chain | protein | 210 | 7% helix, 51% strand | — |
| B | Ly-COV488 Fab light chain | protein | 211 | 6% helix, 53% strand | — |
| C | Spike protein S1 | protein | 195 | 17% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- PRO · Proline · ligand · chains C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.60 | 0.74 | 55 | empty |
| 2 | 190 | 0.57 | 0.80 | 27 | empty |
| 3 | 257 | 0.56 | 0.78 | 31 | empty |
| 4 | 54 | 0.37 | 0.80 | 20 | empty |
| 5 | 86 | 0.37 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1709 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 700 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 317 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7KMH · LY-CoV488 neutralizing antibody against SARS-CoV-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 7KMH · PDBe 7KMH · UniProt P0DTC2
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