Research workbench
Crystal structure of receptor binding domain of SARS-cov-2 spike glycoprotein in ternary complex with EY6A Fab and a nanobody.
Analyse Crystal structure of receptor binding domain of SARS-cov-2 spike glycoprotein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZCZ
- Type
- protein
- Length
- 754 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Nanobody; EY6A heavy chain; EY6A light chain
- UniProt
- P0DTC2
- Ligands
- NAG, MG, CL
- Pockets
- 6 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Spike protein S1 | protein | 195 | 12% helix, 31% strand | P0DTC2 |
| F | Nanobody | protein | 125 | 9% helix, 50% strand | — |
| H | EY6A heavy chain | protein | 219 | 5% helix, 48% strand | — |
| L | EY6A light chain | protein | 215 | 6% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
- MG · Magnesium ion · metal · chains H, L
- CL · Chloride ion · ion · 5 copies · chains E, F, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.52 | 0.76 | 36 | empty |
| 2 | 107 | 0.48 | 0.80 | 19 | empty |
| 3 | 144 | 0.46 | 0.77 | 35 | empty |
| 4 | 185 | 0.46 | 0.75 | 28 | empty |
| 5 | 205 | 0.45 | 0.74 | 28 | CL |
Interfaces
4 interfaces between chains.
- H–L · 2054 Ų buried · 10 hydrogen bonds · protein-protein
- E–H · 637 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 621 Ų buried · 10 hydrogen bonds · protein-protein
- E–L · 481 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6ZCZ · Crystal structure of receptor binding domain of SARS-CoV-2 Spike glycoprotein in ternary… · 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 6ZCZ · PDBe 6ZCZ · UniProt P0DTC2
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