MolNFT v1 · #180006 · protein
Ly-COV555 neutralizing antibody against SARS-cov-2
7KMG · Ly-COV555 Fab heavy chain: “Ly-COV555 neutralizing antibody against SARS-cov-2”. X-ray diffraction, 15 pockets (best druggability 0.73). MolNFT v1 #180006 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KMG
- Type
- protein
- Length
- 1,255 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ly-COV555 Fab heavy chain; Ly-COV555 Fab light chain; Spike protein S1
- UniProt
- P0DTC2
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ly-COV555 Fab heavy chain | protein | 225 | 10% helix, 50% strand | — |
| B, E | Ly-COV555 Fab light chain | protein | 212 | 5% helix, 51% strand | — |
| C | Spike protein S1 | protein | 193 | 15% helix, 30% strand | P0DTC2 |
| D | Ly-COV555 Fab heavy chain | protein | 222 | 8% helix, 50% strand | — |
| F | Spike protein S1 | protein | 191 | 16% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.73 | 0.76 | 98 | empty |
| 2 | 107 | 0.65 | 0.89 | 33 | empty |
| 3 | 385 | 0.57 | 0.75 | 51 | empty |
| 4 | 264 | 0.56 | 0.77 | 38 | empty |
| 5 | 235 | 0.56 | 0.78 | 48 | empty |
Interfaces
11 interfaces between chains.
- A–B · 2097 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1970 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 649 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 632 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 528 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 7KMG · LY-CoV555 neutralizing antibody against SARS-CoV-2 · the same entry in another collection · chain C against C, 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 7KMG · PDBe 7KMG · UniProt P0DTC2
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