MolNFT v1 · #180434 · protein
Potent SARS-cov-2 binding and neutralization through maturation of iconic SARS-cov-1ANTIBODIES
7KZA · Fab fragment heavy chain of anti-COV2-rbd antibody variant…: “Potent SARS-cov-2 binding and neutralization through maturation of iconic SARS-cov-1ANTIBODIES”. X-ray diffraction, 3 ligands (NA, CL, PO4), 5 pockets (best druggability…
- PDB
- 7KZA
- Type
- protein
- Length
- 428 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab fragment heavy chain of anti-COV2-rbd antibody variant CR3022-B6; Fab fragment light…
- Ligands
- NA, CL, PO4
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab fragment heavy chain of anti-COV2-rbd antibody variant CR3022-B6 | protein | 215 | 8% helix, 52% strand | — |
| L | Fab fragment light chain of anti-COV2-rbd antibody variant CR3022-B6 | protein | 213 | 6% helix, 50% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains L
- CL · Chloride ion · ion · 2 copies · chains H, L
- PO4 · Phosphate ion · ion · chains H, L
- GOL · Glycerol · additive · 5 copies · chains H, L
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 | 365 | 0.55 | 0.74 | 44 | PO4 |
| 2 | 59 | 0.52 | 0.87 | 24 | GOL |
| 3 | 80 | 0.31 | 0.73 | 22 | empty |
| 4 | 56 | 0.31 | 0.76 | 15 | CL |
| 5 | 57 | 0.31 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- H–L · 1817 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7KZA · 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 7KZA · PDBe 7KZA
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