Research workbench
Cryo-electron microscopy structure of mouse coronavirus spike protein complexed with its murine receptor
Analyse Cryo-electron microscopy structure of mouse coronavirus spike protein complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VSJ
- Type
- protein
- Length
- 3,687 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Carcinoembryonic antigen-related cell adhesion molecule 1
- UniProt
- P11224, P31809
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 20% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1122 | 22% helix, 22% strand | P11224 |
| D, E, F | Carcinoembryonic antigen-related cell adhesion molecule 1 | protein | 107 | 6% helix, 48% strand | P31809 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, D, B, E, C, F
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 | 1049 | 0.85 | 0.86 | 105 | empty |
| 2 | 817 | 0.82 | 0.85 | 125 | empty |
| 3 | 861 | 0.82 | 0.85 | 91 | empty |
| 4 | 700 | 0.82 | 0.86 | 76 | empty |
| 5 | 481 | 0.80 | 0.88 | 60 | empty |
Interfaces
9 interfaces between chains.
- B–C · 6015 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 6000 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 5991 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 879 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 879 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 6VSJ · Cryo-electron microscopy structure of mouse coronavirus spike protein complexed with its… · the same entry in another collection · chain F against F, TM-score 1.00
- P31809 · AlphaFold monomer V2.0 prediction for carcinoembryonic antigen- related cell adhesion… · a predicted model of the same protein · chain F against A, TM-score 0.96
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 P11224
- Every structure of UniProt P31809
- Elsewhere: RCSB PDB 6VSJ · PDBe 6VSJ · UniProt P11224 · UniProt P31809
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