Research workbench
Cryoem structure of SARS-cov-2 S protein in complex with receptor binding domain antibody DH1042
Analyse Cryoem structure of SARS-cov-2 S protein in complex with receptor binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7THT
- Type
- protein
- Length
- 3,651 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; DH1042 heavy chain; DH1042 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | Spike glycoprotein | protein | 991 | 24% helix, 33% strand | P0DTC2 |
| V | Spike glycoprotein | protein | 986 | 23% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 990 | 23% helix, 32% strand | P0DTC2 |
| H, a, d | DH1042 heavy chain | protein | 122 | 2% helix, 48% strand | — |
| L, c, b | DH1042 light chain | protein | 106 | 3% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 59 copies · chains S, V, C
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.86 | 0.87 | 147 | empty |
| 2 | 720 | 0.84 | 0.87 | 94 | empty |
| 3 | 713 | 0.80 | 0.84 | 73 | empty |
| 4 | 1046 | 0.78 | 0.80 | 86 | empty |
| 5 | 118 | 0.76 | 0.96 | 24 | empty |
Interfaces
13 interfaces between chains.
- S–C · 4953 Ų buried · 47 hydrogen bonds · protein-protein
- S–V · 4703 Ų buried · 45 hydrogen bonds · protein-protein
- V–C · 4360 Ų buried · 39 hydrogen bonds · protein-protein
- S–a · 865 Ų buried · 12 hydrogen bonds · protein-protein
- a–c · 851 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 glycan, 29 disulfide (N-glycosylation, disulfide).
Compared structures
- 7THT · CryoEM structure of SARS-CoV-2 S protein in complex with Receptor Binding Domain antibody… · the same entry in another collection · chain S against S, 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 7THT · PDBe 7THT · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.