MolNFT v1 · #181152 · protein
Crystal structure of SARS-cov-2 spike protein receptor-binding domain in complex with two cross-neutralizing antibodies CV38-142 and COVA1- 16 fabs isolated from COVID-19 patients
7LM8 · Spike protein S1: “Crystal structure of SARS-cov-2 spike protein receptor-binding domain in complex with two cross-neutralizing…”. X-ray diffraction, 3 ligands (NAG, BMA, FUC), 17 pockets (best druggability 0.68). MolNFT v1 #181152…
- PDB
- 7LM8
- Type
- protein
- Length
- 1,071 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; COVA1-16 Fab heavy chain; COVA1-16 Fab light chain; CV38-142 Fab heavy…
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, FUC
- Pockets
- 17 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 196 | 18% helix, 30% strand | P0DTC2 |
| H | COVA1-16 Fab heavy chain | protein | 226 | 9% helix, 50% strand | — |
| L | COVA1-16 Fab light chain | protein | 213 | 6% helix, 52% strand | — |
| M | CV38-142 Fab heavy chain | protein | 219 | 8% helix, 52% strand | — |
| N | CV38-142 Fab light chain | protein | 217 | 7% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, M, N
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A, M, N
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, H, M, L, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 806 | 0.68 | 0.75 | 65 | empty |
| 2 | 51 | 0.64 | 0.95 | 16 | EDO |
| 3 | 87 | 0.61 | 0.88 | 18 | EDO |
| 4 | 533 | 0.60 | 0.74 | 54 | empty |
| 5 | 292 | 0.57 | 0.77 | 44 | EDO |
Interfaces
6 interfaces between chains.
- M–N · 2082 Ų buried · 29 hydrogen bonds · protein-protein
- H–L · 1665 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 708 Ų buried · 14 hydrogen bonds · protein-protein
- A–M · 655 Ų buried · 8 hydrogen bonds · protein-protein
- A–N · 170 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7LM8 · Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with two… · 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 7LM8 · PDBe 7LM8 · UniProt P0DTC2
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