MolNFT v1 · #177166 · protein
Cryo-EM structure of the SARS-cov-2 S-6P in complex with 35B5 FAB(STATE2, local refinement of the rbd and 35B5 Fab)
7E9P · Spike glycoprotein: “Cryo-EM structure of the SARS-cov-2 S-6P in complex with 35B5 FAB(STATE2, local refinement of the rbd and…”. Electron microscopy, 1 ligand (NAG), 7 pockets (best druggability 0.52). MolNFT v1 #177166 on…
- PDB
- 7E9P
- Type
- protein
- Length
- 639 residues
- Chains
- 3
- 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
- 7 · best druggability 0.52
Structure
electron microscopy · 3 distinct chains · 6% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Spike glycoprotein | protein | 195 | 14% helix, 24% strand | P0DTC2 |
| L | Light chain of 35B5 Fab | protein | 218 | 1% helix, 45% strand | — |
| H | Heavy chain of 35B5 Fab | protein | 226 | 3% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.52 | 0.80 | 22 | empty |
| 2 | 167 | 0.47 | 0.76 | 27 | empty |
| 3 | 204 | 0.46 | 0.74 | 30 | empty |
| 4 | 179 | 0.44 | 0.74 | 26 | empty |
| 5 | 61 | 0.40 | 0.81 | 14 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1677 Ų buried · 5 hydrogen bonds · protein-protein
- B–H · 1075 Ų buried · 10 hydrogen bonds · protein-protein
- B–L · 33 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7E9P · Cryo-EM structure of the SARS-CoV-2 S-6P in complex with 35B5 Fab(state2, local… · 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 7E9P · PDBe 7E9P · UniProt P0DTC2
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