MolNFT v1 · #181153 · protein
Crystal structure of SARS-cov spike protein receptor-binding domain in complex with a cross-neutralizing antibody CV38-142 Fab isolated from COVID-19 patient
7LM9 · Spike glycoprotein: “Crystal structure of SARS-cov spike protein receptor-binding domain in complex with a cross-neutralizing…”. X-ray diffraction, 3 ligands (NAG, BMA, FUC), 9 pockets (best druggability 0.59). MolNFT v1 #181153 on…
- PDB
- 7LM9
- Type
- protein
- Length
- 634 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; CV38-142 Fab heavy chain; CV38-142 Fab light chain
- UniProt
- D2E265
- Ligands
- NAG, BMA, FUC
- Pockets
- 9 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 192 | 19% helix, 30% strand | D2E265 |
| H | CV38-142 Fab heavy chain | protein | 226 | 12% helix, 51% strand | — |
| L | CV38-142 Fab light chain | protein | 216 | 7% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, H, L
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A, H, L
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.59 | 0.86 | 18 | EDO |
| 2 | 53 | 0.54 | 0.89 | 19 | EDO |
| 3 | 316 | 0.53 | 0.74 | 40 | empty |
| 4 | 104 | 0.52 | 0.82 | 28 | EDO |
| 5 | 80 | 0.37 | 0.76 | 17 | NAG, EDO |
Interfaces
3 interfaces between chains.
- H–L · 2223 Ų buried · 28 hydrogen bonds · protein-protein
- A–H · 576 Ų buried · 6 hydrogen bonds · protein-protein
- A–L · 198 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7LM9 · Crystal structure of SARS-CoV spike protein receptor-binding domain in complex with a… · 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 D2E265
- Elsewhere: RCSB PDB 7LM9 · PDBe 7LM9 · UniProt D2E265
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