Research workbench
SARS-cov-2 SPIKE:5A6 Fab complex I focused refinement
Analyse SARS-cov-2 SPIKE:5A6 Fab complex I focused refinement in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M71
- Type
- protein
- Length
- 852 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Antibody 5A6 Fab heavy chain; Antibody 5A6 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.61
Structure
electron microscopy · 3 distinct chains · 9% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike glycoprotein | protein | 209 | 15% helix, 27% strand | P0DTC2 |
| H | Antibody 5A6 Fab heavy chain | protein | 220 | 8% helix, 47% strand | — |
| L | Antibody 5A6 Fab light chain | protein | 214 | 5% helix, 37% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.61 | 0.82 | 40 | empty |
| 2 | 348 | 0.57 | 0.75 | 36 | empty |
| 3 | 176 | 0.50 | 0.77 | 39 | empty |
| 4 | 179 | 0.45 | 0.74 | 21 | empty |
| 5 | 72 | 0.38 | 0.78 | 16 | empty |
Interfaces
4 interfaces between chains.
- H–L · 2183 Ų buried · 23 hydrogen bonds · protein-protein
- A–H · 725 Ų buried · 7 hydrogen bonds · protein-protein
- B–L · 393 Ų buried · 5 hydrogen bonds · protein-protein
- A–L · 281 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7M71 · SARS-CoV-2 Spike:5A6 Fab complex I focused refinement · 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 7M71 · PDBe 7M71 · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.