Research workbench
Local cryoem structure of the SARS-cov-2 S6PV2 in complex with bd-804 Fab
Analyse Local cryoem structure of the SARS-cov-2 S6PV2 in complex with bd-804 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EYA
- Type
- protein
- Length
- 576 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Bd-804L; Bd-804H
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 5 · best druggability 0.49
Structure
electron microscopy · 4 distinct chains · 6% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Spike glycoprotein | protein | 183 | 18% helix, 23% strand | P0DTC2 |
| L | Bd-804L | protein | 103 | 0% helix, 31% strand | — |
| H | Bd-804H | protein | 125 | 2% helix, 34% strand | — |
| N | Spike glycoprotein | protein | 165 | 0% helix, 46% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains L, N
- BMA · beta-D-mannopyranose · sugar · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.49 | 0.78 | 30 | empty |
| 2 | 64 | 0.40 | 0.80 | 17 | empty |
| 3 | 51 | 0.37 | 0.81 | 18 | empty |
| 4 | 63 | 0.28 | 0.74 | 19 | empty |
| 5 | 64 | 0.28 | 0.73 | 12 | empty |
Interfaces
5 interfaces between chains.
- L–H · 805 Ų buried · 5 hydrogen bonds · protein-protein
- R–L · 722 Ų buried · 7 hydrogen bonds · protein-protein
- R–H · 476 Ų buried · 6 hydrogen bonds · protein-protein
- R–N · 130 Ų buried · 2 hydrogen bonds · protein-protein
- L–N · 38 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7EYA · Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-804 Fab · the same entry in another collection · chain H against H, 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 7EYA · PDBe 7EYA · UniProt P0DTC2
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