Research workbench
Structure of SARS-cov-2 S protein in complex with receptor binding domain antibody DH1041
Analyse Structure of SARS-cov-2 S protein in complex with receptor binding domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LAA
- Type
- protein
- Length
- 3,002 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; DH1041 heavy chain; DH1041 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 991 | 22% helix, 32% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 788 | 26% helix, 32% strand | P0DTC2 |
| H | DH1041 heavy chain | protein | 217 | 6% helix, 32% strand | — |
| L | DH1041 light chain | protein | 217 | 7% helix, 34% strand | — |
| C | Spike glycoprotein | protein | 789 | 26% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 51 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 6 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.83 | 0.84 | 118 | empty |
| 2 | 758 | 0.81 | 0.85 | 65 | empty |
| 3 | 563 | 0.81 | 0.87 | 55 | empty |
| 4 | 782 | 0.80 | 0.84 | 84 | empty |
| 5 | 553 | 0.74 | 0.82 | 40 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4523 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 4228 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 4164 Ų buried · 40 hydrogen bonds · protein-protein
- H–L · 2027 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 674 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 glycan, 31 disulfide (N-glycosylation, disulfide).
Compared structures
- 7LAA · Structure of SARS-CoV-2 S protein in complex with Receptor Binding Domain antibody DH1041 · 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 7LAA · PDBe 7LAA · UniProt P0DTC2
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