Research workbench
SARS-cov-2 spike glycoprotein in complex with a neutralizing antibody EY6A Fab
Analyse SARS-cov-2 spike glycoprotein in complex with a neutralizing antibody EY6A Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZDH
- Type
- protein
- Length
- 4,308 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; EY6A heavy chain; EY6A light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1002 | 23% helix, 32% strand | P0DTC2 |
| H, D, G | EY6A heavy chain | protein | 219 | 4% helix, 49% strand | — |
| L, F, I | EY6A light chain | protein | 215 | 8% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 49 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.86 | 0.87 | 152 | empty |
| 2 | 726 | 0.86 | 0.90 | 98 | empty |
| 3 | 532 | 0.79 | 0.85 | 88 | empty |
| 4 | 570 | 0.73 | 0.81 | 44 | empty |
| 5 | 710 | 0.71 | 0.78 | 53 | empty |
Interfaces
18 interfaces between chains.
- B–C · 4385 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 4341 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 4283 Ų buried · 33 hydrogen bonds · protein-protein
- H–L · 1842 Ų buried · 7 hydrogen bonds · protein-protein
- G–I · 1608 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 disulfide, 36 glycan (disulfide, N-glycosylation).
Compared structures
- 6ZDH · SARS-CoV-2 Spike glycoprotein in complex with a neutralizing antibody EY6A Fab · 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 6ZDH · PDBe 6ZDH · UniProt P0DTC2
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