Research workbench
SARS-cov-2 spike rbd in complex with neutralizing Fab 2H04 (local refinement)
Analyse SARS-cov-2 spike rbd in complex with neutralizing Fab 2H04 (local refinement) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K9K
- Type
- protein
- Length
- 402 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; 2H04 heavy chain; 2H04 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, FUC
- Pockets
- 3 · best druggability 0.55
Structure
electron microscopy · 3 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 175 | 17% helix, 30% strand | P0DTC2 |
| H | 2H04 heavy chain | protein | 121 | 2% helix, 52% strand | — |
| L | 2H04 light chain | protein | 106 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, H
- BMA · beta-D-mannopyranose · sugar · chains H
- FUC · alpha-L-fucopyranose · sugar · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.55 | 0.78 | 22 | empty |
| 2 | 175 | 0.46 | 0.75 | 24 | NAG |
| 3 | 55 | 0.26 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- H–L · 837 Ų buried · 4 hydrogen bonds · protein-protein
- A–H · 546 Ų buried · 7 hydrogen bonds · protein-protein
- A–L · 357 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7K9K · SARS-CoV-2 Spike RBD in complex with neutralizing Fab 2H04 (local refinement) · 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 7K9K · PDBe 7K9K · UniProt P0DTC2
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