Research workbench
Crystal structure of SARS-cov-2 antibody with rbd
Analyse Crystal structure of SARS-cov-2 antibody with rbd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BWJ
- Type
- protein
- Length
- 636 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Antibody light chain; Antibody heavy chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Spike protein S1 | protein | 194 | 17% helix, 29% strand | P0DTC2 |
| L | Antibody light chain | protein | 213 | 7% helix, 49% strand | — |
| H | Antibody heavy chain | protein | 229 | 5% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.64 | 0.74 | 74 | empty |
| 2 | 153 | 0.45 | 0.76 | 23 | empty |
| 3 | 176 | 0.44 | 0.74 | 28 | empty |
| 4 | 143 | 0.41 | 0.74 | 24 | empty |
| 5 | 90 | 0.38 | 0.76 | 22 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1897 Ų buried · 17 hydrogen bonds · protein-protein
- E–H · 520 Ų buried · 6 hydrogen bonds · protein-protein
- E–L · 163 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7BWJ · crystal structure of SARS-CoV-2 antibody with RBD · the same entry in another collection · chain E against E, 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 7BWJ · PDBe 7BWJ · UniProt P0DTC2
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