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Crystal structure of SARS-cov-2 receptor binding domain in complex with neutralizing antibody K398.22
Analyse Crystal structure of SARS-cov-2 receptor binding domain 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
- 7TP4
- Type
- protein
- Length
- 624 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; K398.22 heavy chain; K398.22 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z | Spike protein S1 | protein | 194 | 18% helix, 29% strand | P0DTC2 |
| H | K398.22 heavy chain | protein | 219 | 7% helix, 54% strand | — |
| L | K398.22 light chain | protein | 211 | 7% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains Z
- FUC · alpha-L-fucopyranose · sugar
- EDO · 1,2-ethanediol · additive · chains Z, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.63 | 0.76 | 53 | empty |
| 2 | 261 | 0.53 | 0.76 | 34 | EDO |
| 3 | 144 | 0.43 | 0.75 | 27 | empty |
| 4 | 89 | 0.35 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1699 Ų buried · 19 hydrogen bonds · protein-protein
- Z–H · 661 Ų buried · 14 hydrogen bonds · protein-protein
- Z–L · 222 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7TP4 · Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing… · the same entry in another collection · chain Z against Z, 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 7TP4 · PDBe 7TP4 · UniProt P0DTC2
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