Research workbench
Ly-COV1404 neutralizing antibody against SARS-cov-2
Analyse Ly-COV1404 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
- 7MMO
- Type
- protein
- Length
- 1,217 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ly-COV1404 Fab heavy chain; Ly-COV1404 Fab light chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ly-COV1404 Fab heavy chain | protein | 212 | 7% helix, 50% strand | — |
| B, E | Ly-COV1404 Fab light chain | protein | 214 | 7% helix, 51% strand | — |
| C | Spike protein S1 | protein | 194 | 17% helix, 31% strand | P0DTC2 |
| D | Ly-COV1404 Fab heavy chain | protein | 208 | 6% helix, 51% strand | — |
| F | Spike protein S1 | protein | 175 | 13% helix, 31% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.79 | 0.81 | 84 | empty |
| 2 | 517 | 0.60 | 0.74 | 58 | empty |
| 3 | 390 | 0.55 | 0.74 | 45 | empty |
| 4 | 208 | 0.54 | 0.78 | 22 | empty |
| 5 | 152 | 0.43 | 0.74 | 26 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1728 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1726 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 524 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 444 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 402 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 2 modified, 1 glycan (disulfide, cyclization, N-glycosylation).
Compared structures
- 7MMO · LY-CoV1404 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 7MMO · PDBe 7MMO · UniProt P0DTC2
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