MolNFT v1 · #180606 · protein
Cryo-EM structure of the SARS-cov-2 spike glycoprotein bound to Fab H4
7L58: “Cryo-EM structure of the SARS-cov-2 spike glycoprotein bound to Fab H4”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.83). MolNFT v1 #180606 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7L58
- Type
- protein
- Length
- 3,442 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Fab H4 variable domain heavy chain; Fab H4 variable domain light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1069 | 21% helix, 30% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1071 | 21% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1067 | 22% helix, 30% strand | P0DTC2 |
| H | Fab H4 variable domain heavy chain | protein | 123 | 5% helix, 47% strand | — |
| L | Fab H4 variable domain light chain | protein | 112 | 3% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 41 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 | 1043 | 0.83 | 0.84 | 176 | empty |
| 2 | 942 | 0.81 | 0.83 | 153 | empty |
| 3 | 984 | 0.80 | 0.82 | 108 | empty |
| 4 | 1060 | 0.79 | 0.81 | 141 | empty |
| 5 | 1046 | 0.79 | 0.81 | 149 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1512 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1484 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1379 Ų buried · 7 hydrogen bonds · protein-protein
- H–L · 385 Ų buried · 3 hydrogen bonds · protein-protein
- B–H · 217 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 37 glycan (disulfide, N-glycosylation).
Compared structures
- 7L58 · Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab H4 · 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 7L58 · PDBe 7L58 · UniProt P0DTC2
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