MolNFT v2 · #224621 · protein
Crystal structure of JM-1A in complex with SARS-CoV-2 RBD
8X0Y · Spike protein S1: “Crystal structure of JM-1A in complex with SARS-CoV-2 RBD”. X-ray diffraction at 1.94, 4 ligands (NAG, FUC, CL), 12 pockets (best druggability 0.81). MolNFT v2 #224621 on GenesisL1: 3D structure, binding sites and…
- PDB
- 8X0Y
- Type
- protein
- Length
- 1,247 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.94
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike protein S1; Heavy chain of JM-1A Fab; Light chain of JM-1A Fab
- UniProt
- P0DTC2
- Ligands
- NAG, FUC, CL, PO4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.94 · 5 distinct chains · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Spike protein S1 | protein | 195 | 17% helix, 29% strand | P0DTC2 |
| E | Heavy chain of JM-1A Fab | protein | 219 | 7% helix, 52% strand | — |
| F, I | Light chain of JM-1A Fab | protein | 212 | 6% helix, 52% strand | — |
| A | Spike protein S1 | protein | 192 | 19% helix, 30% strand | P0DTC2 |
| G | Heavy chain of JM-1A Fab | protein | 217 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A
- FUC · alpha-L-fucopyranose · sugar · 2 copies
- CL · Chloride ion · ion · chains B
- PO4 · Phosphate ion · ion
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.81 | 0.83 | 161 | empty |
| 2 | 852 | 0.68 | 0.74 | 66 | empty |
| 3 | 545 | 0.59 | 0.73 | 60 | empty |
| 4 | 77 | 0.56 | 0.88 | 19 | empty |
| 5 | 175 | 0.50 | 0.77 | 27 | empty |
Interfaces
10 interfaces between chains.
- G–I · 1689 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1620 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 776 Ų buried · 13 hydrogen bonds · protein-protein
- A–G · 737 Ų buried · 8 hydrogen bonds · protein-protein
- B–A · 682 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, cyclization).
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 8X0Y · PDBe 8X0Y · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.