Research workbench
Crystal structure of SARS-cov-2 rbd in complex with a neutralizing antibody scfv
Analyse Crystal structure of SARS-cov-2 rbd in complex with a neutralizing antibody scfv in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DEO
- Type
- protein
- Length
- 871 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody scfv; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG, CA
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody scfv | protein | 241 | 6% helix, 47% strand | — |
| B | Spike protein S1 | protein | 202 | 15% helix, 29% strand | P0DTC2 |
| C | Antibody scfv | protein | 234 | 4% helix, 49% strand | — |
| D | Spike protein S1 | protein | 194 | 18% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, D
- CA · Calcium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.76 | 0.80 | 104 | empty |
| 2 | 361 | 0.66 | 0.80 | 34 | empty |
| 3 | 204 | 0.56 | 0.79 | 40 | empty |
| 4 | 134 | 0.53 | 0.81 | 30 | empty |
| 5 | 82 | 0.51 | 0.84 | 16 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1065 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1063 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 463 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 228 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 217 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7DEO · Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv · 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 7DEO · PDBe 7DEO · UniProt P0DTC2
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