Research workbench
Crystal structure of SARS-cov-2 S receptor-binding domain (rbd) in complex COV11 Fab
Analyse Crystal structure of SARS-cov-2 S receptor-binding domain (rbd) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S4S
- Type
- protein
- Length
- 627 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; COV11 heavy chain; COV11 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, SO4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 193 | 18% helix, 31% strand | P0DTC2 |
| H | COV11 heavy chain | protein | 219 | 11% helix, 51% strand | — |
| L | COV11 light chain | protein | 215 | 7% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A, H, L
- ACT · Acetate ion · additive · 4 copies · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.67 | 0.85 | 25 | empty |
| 2 | 65 | 0.63 | 0.92 | 27 | empty |
| 3 | 386 | 0.55 | 0.74 | 49 | empty |
| 4 | 167 | 0.47 | 0.76 | 26 | ACT |
| 5 | 99 | 0.35 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1702 Ų buried · 13 hydrogen bonds · protein-protein
- A–H · 884 Ų buried · 19 hydrogen bonds · protein-protein
- A–L · 391 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7S4S · Crystal Structure of SARS-CoV-2 S receptor-binding domain (RBD) in complex CoV11 Fab · the same entry in another collection · chain L against L, 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 7S4S · PDBe 7S4S · UniProt P0DTC2
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