MolNFT v1 · #181365 · protein
Cryo-EM structure of the SARS-cov-2 spike glycoprotein bound to Fab 2- 7
7LSS: “Cryo-EM structure of the SARS-cov-2 spike glycoprotein bound to Fab 2- 7”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.82). MolNFT v1 #181365 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LSS
- Type
- protein
- Length
- 2,783 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Fab 2-7 variable light chain; Fab 2-7 variable heavy chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 779 | 26% helix, 34% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 992 | 23% helix, 33% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 785 | 25% helix, 34% strand | P0DTC2 |
| L | Fab 2-7 variable light chain | protein | 108 | 6% helix, 44% strand | — |
| H | Fab 2-7 variable heavy chain | protein | 119 | 5% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 42 copies · chains A, B, C
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 | 852 | 0.82 | 0.84 | 114 | empty |
| 2 | 824 | 0.81 | 0.84 | 77 | empty |
| 3 | 1185 | 0.81 | 0.82 | 113 | empty |
| 4 | 637 | 0.72 | 0.79 | 55 | empty |
| 5 | 68 | 0.70 | 0.96 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3999 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 3412 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 3318 Ų buried · 29 hydrogen bonds · protein-protein
- L–H · 906 Ų buried · 8 hydrogen bonds · protein-protein
- B–H · 485 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 glycan, 33 disulfide (N-glycosylation, disulfide).
Compared structures
- 7LSS · Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab 2-7 · 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 7LSS · PDBe 7LSS · UniProt P0DTC2
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