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Crystallographic structure of neutralizing antibody 10-40 in complex with SARS-cov-2 spike receptor binding domain
Analyse Crystallographic structure of neutralizing antibody 10-40 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SD5
- Type
- protein
- Length
- 633 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; 10-40 heavy chain; 10-40 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 193 | 19% helix, 30% strand | P0DTC2 |
| H | 10-40 heavy chain | protein | 227 | 8% helix, 50% strand | — |
| L | 10-40 light chain | protein | 213 | 8% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.60 | 0.74 | 62 | empty |
| 2 | 319 | 0.57 | 0.76 | 47 | empty |
| 3 | 224 | 0.49 | 0.75 | 38 | empty |
| 4 | 90 | 0.46 | 0.80 | 17 | empty |
| 5 | 56 | 0.39 | 0.81 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1719 Ų buried · 22 hydrogen bonds · protein-protein
- A–H · 733 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 277 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7SD5 · Crystallographic structure of neutralizing antibody 10-40 in complex with 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 7SD5 · PDBe 7SD5 · UniProt P0DTC2
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