Research workbench
Cryo-EM structure of the SARS-cov-2 N501Y mutant spike protein ectodomain bound to Fab AB1 (class 2)
Analyse Cryo-EM structure of the SARS-cov-2 N501Y mutant spike protein ectodomain bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MJK
- Type
- protein
- Length
- 4,389 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Fab AB1 heavy chain; Fab AB1 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 17% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1040 | 21% helix, 34% strand | P0DTC2 |
| D, F, H | Fab AB1 heavy chain | protein | 210 | 4% helix, 51% strand | — |
| E, G, I | Fab AB1 light chain | protein | 213 | 6% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 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 | 908 | 0.86 | 0.88 | 113 | empty |
| 2 | 380 | 0.83 | 0.91 | 63 | empty |
| 3 | 412 | 0.77 | 0.86 | 61 | empty |
| 4 | 629 | 0.74 | 0.81 | 45 | empty |
| 5 | 613 | 0.72 | 0.80 | 43 | empty |
Interfaces
18 interfaces between chains.
- A–B · 4403 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 4398 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 4394 Ų buried · 37 hydrogen bonds · protein-protein
- G–F · 1716 Ų buried · 13 hydrogen bonds · protein-protein
- I–H · 1716 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 disulfide, 42 glycan (disulfide, N-glycosylation).
Compared structures
- 7MJK · Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to Fab… · the same entry in another collection · chain C against C, 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 7MJK · PDBe 7MJK · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.