Research workbench
Association of three complexes of largely structurally disordered spike ectodomain with bound EY6A Fab
Analyse Association of three complexes of largely structurally disordered spike… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZDG
- Type
- protein
- Length
- 1,884 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; EY6A heavy chain; EY6A light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.62
Structure
electron microscopy · 3 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, A, D | Spike protein S1 | protein | 194 | 12% helix, 31% strand | P0DTC2 |
| H, B, F | EY6A heavy chain | protein | 219 | 4% helix, 48% strand | — |
| L, C, G | EY6A light chain | protein | 215 | 8% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains E, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.62 | 0.77 | 57 | empty |
| 2 | 245 | 0.61 | 0.80 | 39 | empty |
| 3 | 227 | 0.56 | 0.78 | 32 | empty |
| 4 | 357 | 0.55 | 0.74 | 39 | empty |
| 5 | 289 | 0.51 | 0.74 | 40 | empty |
Interfaces
15 interfaces between chains.
- F–G · 1955 Ų buried · 9 hydrogen bonds · protein-protein
- H–L · 1889 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 1805 Ų buried · 3 hydrogen bonds · protein-protein
- E–H · 597 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 587 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6ZDG · Association of three complexes of largely structurally disordered Spike ectodomain with… · 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 6ZDG · PDBe 6ZDG · UniProt P0DTC2
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