MolNFT v1 · #180436 · protein
Potent SARS-cov-2 binding and neutralization through maturation of iconic SARS-cov-1ANTIBODIES
7KZC · Fab heavy chain of M396-B10 antibody: “Potent SARS-cov-2 binding and neutralization through maturation of iconic SARS-cov-1ANTIBODIES”. X-ray diffraction, 1 ligand (CL), 10 pockets (best druggability 0.74). MolNFT v1 #180436 on…
- PDB
- 7KZC
- Type
- protein
- Length
- 825 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain of M396-B10 antibody; Fab light chain of M396-B10 antibody
- Ligands
- CL
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab heavy chain of M396-B10 antibody | protein | 205 | 7% helix, 53% strand | — |
| L | Fab light chain of M396-B10 antibody | protein | 215 | 7% helix, 49% strand | — |
| C | Fab heavy chain of M396-B10 antibody | protein | 192 | 8% helix, 51% strand | — |
| D | Fab light chain of M396-B10 antibody | protein | 213 | 8% helix, 50% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.74 | 0.80 | 85 | empty |
| 2 | 215 | 0.54 | 0.78 | 37 | empty |
| 3 | 345 | 0.52 | 0.73 | 49 | empty |
| 4 | 53 | 0.52 | 0.88 | 23 | empty |
| 5 | 74 | 0.50 | 0.84 | 22 | empty |
Interfaces
5 interfaces between chains.
- H–L · 1637 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1610 Ų buried · 16 hydrogen bonds · protein-protein
- H–D · 435 Ų buried · 10 hydrogen bonds · protein-protein
- L–D · 72 Ų buried · 0 hydrogen bonds · protein-protein
- H–C · 60 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7KZC · Potent SARS-CoV-2 binding and neutralization through maturation of iconic… · 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 7KZC · PDBe 7KZC
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