MolNFT v1 · #177595 · protein
Cryo-EM structure of the SARS-cov-2 S-6P in complex with FAB30 (local refinement of the rbd and FAB30)
7ENG · Light chain of FAB30: “Cryo-EM structure of the SARS-cov-2 S-6P in complex with FAB30 (local refinement of the rbd and FAB30)”. Electron microscopy, 1 ligand (NAG), 6 pockets (best druggability 0.63). MolNFT v1 #177595 on GenesisL1…
- PDB
- 7ENG
- Type
- protein
- Length
- 640 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of FAB30; Heavy chain of FAB30; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.63
Structure
electron microscopy · 3 distinct chains · 8% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Light chain of FAB30 | protein | 219 | 5% helix, 40% strand | — |
| H | Heavy chain of FAB30 | protein | 226 | 5% helix, 46% strand | — |
| B | Spike glycoprotein | protein | 195 | 14% helix, 23% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.63 | 0.93 | 20 | empty |
| 2 | 396 | 0.59 | 0.75 | 52 | empty |
| 3 | 236 | 0.55 | 0.78 | 29 | empty |
| 4 | 132 | 0.49 | 0.79 | 24 | empty |
| 5 | 101 | 0.36 | 0.74 | 25 | empty |
Interfaces
3 interfaces between chains.
- L–H · 2014 Ų buried · 8 hydrogen bonds · protein-protein
- H–B · 557 Ų buried · 10 hydrogen bonds · protein-protein
- L–B · 432 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7ENG · Cryo-EM structure of the SARS-CoV-2 S-6P in complex with Fab30 (local refinement of the… · the same entry in another collection · chain L against L, 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 7ENG · PDBe 7ENG · UniProt P0DTC2
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