MolNFT v1 · #185339 · protein
Crystal structure of the receptor binding domain of SARS-cov-2 spike glycoprotein in complex with fi-3A Fab
7PQY · Spike protein S1: “Crystal structure of the receptor binding domain of SARS-cov-2 spike glycoprotein in complex with fi-3A Fab”. X-ray diffraction, 2 ligands (NAG, FUC), 12 pockets (best druggability 0.66). MolNFT v1 #185339 on…
- PDB
- 7PQY
- Type
- protein
- Length
- 1,232 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Fi-3A Fab heavy chain; Fi-3A Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Spike protein S1 | protein | 189 | 16% helix, 30% strand | P0DTC2 |
| A | Spike protein S1 | protein | 183 | 16% helix, 28% strand | P0DTC2 |
| H, B | Fi-3A Fab heavy chain | protein | 217 | 6% helix, 50% strand | — |
| L, C | Fi-3A Fab light chain | protein | 213 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E
- FUC · alpha-L-fucopyranose · sugar
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 | 229 | 0.66 | 0.84 | 36 | empty |
| 2 | 237 | 0.65 | 0.83 | 36 | empty |
| 3 | 673 | 0.64 | 0.74 | 70 | empty |
| 4 | 547 | 0.61 | 0.74 | 49 | empty |
| 5 | 111 | 0.52 | 0.82 | 16 | empty |
Interfaces
7 interfaces between chains.
- B–C · 1804 Ų buried · 13 hydrogen bonds · protein-protein
- H–L · 1796 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 761 Ų buried · 19 hydrogen bonds · protein-protein
- E–H · 758 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 306 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7PQY · Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in… · the same entry in another collection · chain E against E, 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 7PQY · PDBe 7PQY · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.