Research workbench
Structure of SARS-cov-2 S protein in complex with receptor binding domain antibody DH1047
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
- 7LD1
- Type
- protein
- Length
- 4,249 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; DH1047 heavy chain; DH1047 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 19% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike glycoprotein | protein | 973 | 24% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 949 | 23% helix, 32% strand | P0DTC2 |
| M, P, H | DH1047 heavy chain | protein | 232 | 6% helix, 23% strand | — |
| N, L | DH1047 light chain | protein | 219 | 3% helix, 34% strand | — |
| O | DH1047 light chain | protein | 220 | 10% helix, 30% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 54 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 13 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.83 | 0.84 | 95 | empty |
| 2 | 1069 | 0.83 | 0.84 | 107 | empty |
| 3 | 737 | 0.80 | 0.84 | 90 | empty |
| 4 | 1088 | 0.79 | 0.81 | 111 | empty |
| 5 | 126 | 0.79 | 0.97 | 25 | empty |
Interfaces
13 interfaces between chains.
- A–C · 4305 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 4144 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 4087 Ų buried · 30 hydrogen bonds · protein-protein
- P–O · 1612 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 1388 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 glycan, 34 disulfide (N-glycosylation, disulfide).
Compared structures
- 7LD1 · Structure of SARS-CoV-2 S protein in complex with Receptor Binding Domain antibody DH1047 · 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 7LD1 · PDBe 7LD1 · UniProt P0DTC2
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