Research workbench
Crystal structure of neutralizing antibody 10-28 in complex with SARS- cov-2 spike receptor binding domain (rbd)
Analyse Crystal structure of neutralizing antibody 10-28 in complex with 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
- 7SI2
- Type
- protein
- Length
- 1,860 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 10-28 light chain; 10-28 heavy chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, F, L | 10-28 light chain | protein | 214 | 7% helix, 47% strand | — |
| E, G, H | 10-28 heavy chain | protein | 216 | 7% helix, 52% strand | — |
| A, B, C | Spike protein S1 | protein | 190 | 17% helix, 28% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.61 | 0.76 | 39 | empty |
| 2 | 429 | 0.60 | 0.76 | 35 | empty |
| 3 | 265 | 0.58 | 0.78 | 38 | empty |
| 4 | 202 | 0.57 | 0.80 | 37 | empty |
| 5 | 386 | 0.56 | 0.74 | 62 | empty |
Interfaces
14 interfaces between chains.
- F–G · 1795 Ų buried · 9 hydrogen bonds · protein-protein
- H–L · 1781 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1738 Ų buried · 9 hydrogen bonds · protein-protein
- L–B · 650 Ų buried · 12 hydrogen bonds · protein-protein
- H–A · 545 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7SI2 · Crystal structure of neutralizing antibody 10-28 in complex with SARS-CoV-2 spike… · the same entry in another collection · chain D against D, 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 7SI2 · PDBe 7SI2 · UniProt P0DTC2
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