Research workbench
Cryo-EM structure of the SARS-cov-2 S-6P in complex with FAB30
Analyse Cryo-EM structure of the SARS-cov-2 S-6P in complex with FAB30 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ENF
- Type
- protein
- Length
- 3,390 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Light chain of FAB30; Heavy chain of FAB30
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 20% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 968 | 21% helix, 32% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1001 | 22% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 976 | 23% helix, 31% strand | P0DTC2 |
| O | Light chain of FAB30 | protein | 219 | 5% helix, 43% strand | — |
| P | Heavy chain of FAB30 | protein | 226 | 4% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 53 copies · chains A, B, C, O
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 | 735 | 0.85 | 0.88 | 107 | empty |
| 2 | 1158 | 0.83 | 0.84 | 126 | empty |
| 3 | 944 | 0.82 | 0.84 | 97 | empty |
| 4 | 701 | 0.82 | 0.86 | 67 | empty |
| 5 | 484 | 0.80 | 0.87 | 63 | empty |
Interfaces
7 interfaces between chains.
- B–C · 4606 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 4470 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 4451 Ų buried · 31 hydrogen bonds · protein-protein
- O–P · 1989 Ų buried · 16 hydrogen bonds · protein-protein
- B–P · 567 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 7ENF · Cryo-EM structure of the SARS-CoV-2 S-6P in complex with Fab30 · 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 7ENF · PDBe 7ENF · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.