Research workbench
Cryo-EM structure of the SARS-cov-2 S-6P in complex with 35B5 FAB(3 up rbds, STATE2)
Analyse Cryo-EM structure of the SARS-cov-2 S-6P in complex with 35B5 FAB(3 up rbds… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E9O
- Type
- protein
- Length
- 4,338 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Light chain of 35B5 Fab; Heavy chain of 35B5 Fab
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 16% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Spike glycoprotein | protein | 1002 | 21% helix, 30% strand | P0DTC2 |
| L, O, X | Light chain of 35B5 Fab | protein | 218 | 6% helix, 48% strand | — |
| H, P, Y | Heavy chain of 35B5 Fab | protein | 226 | 3% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains B, C, A
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 | 1004 | 0.87 | 0.88 | 122 | empty |
| 2 | 704 | 0.87 | 0.91 | 90 | empty |
| 3 | 491 | 0.79 | 0.86 | 62 | empty |
| 4 | 858 | 0.76 | 0.80 | 68 | empty |
| 5 | 652 | 0.74 | 0.80 | 41 | empty |
Interfaces
14 interfaces between chains.
- B–C · 4100 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 4071 Ų buried · 24 hydrogen bonds · protein-protein
- B–A · 3971 Ų buried · 25 hydrogen bonds · protein-protein
- O–P · 1841 Ų buried · 13 hydrogen bonds · protein-protein
- L–H · 1620 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 49 disulfide, 27 glycan (disulfide, N-glycosylation).
Compared structures
- 7E9O · Cryo-EM structure of the SARS-CoV-2 S-6P in complex with 35B5 Fab(3 up RBDs, state2) · the same entry in another collection · chain B against B, 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 7E9O · PDBe 7E9O · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.