Research workbench
Cryo-EM structure of SARS-cov-2 spike : H11-H4 Q98R H100E nanobody complex in 2UP1DOWN conformation
Analyse Cryo-EM structure of SARS-cov-2 spike : H11-H4 Q98R H100E nanobody complex in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Z9R
- Type
- protein
- Length
- 3,349 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike GLYCOPROTEIN,FIBRITIN; Nanobody H11-H4 Q98R H100E
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike GLYCOPROTEIN,FIBRITIN | protein | 988 | 22% helix, 32% strand | P0DTC2 |
| B | Spike GLYCOPROTEIN,FIBRITIN | protein | 992 | 23% helix, 32% strand | P0DTC2 |
| C | Spike GLYCOPROTEIN,FIBRITIN | protein | 991 | 22% helix, 33% strand | P0DTC2 |
| Y, X, Z | Nanobody H11-H4 Q98R H100E | protein | 126 | 9% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 66 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 | 980 | 0.87 | 0.88 | 125 | empty |
| 2 | 785 | 0.84 | 0.87 | 79 | empty |
| 3 | 1149 | 0.79 | 0.81 | 112 | empty |
| 4 | 958 | 0.76 | 0.78 | 74 | empty |
| 5 | 514 | 0.76 | 0.84 | 34 | empty |
Interfaces
7 interfaces between chains.
- A–B · 4629 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 4330 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 4127 Ų buried · 25 hydrogen bonds · protein-protein
- B–Y · 711 Ų buried · 11 hydrogen bonds · protein-protein
- C–Z · 704 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide, 42 glycan (disulfide, N-glycosylation).
Compared structures
- 7Z9R · CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-H4 Q98R H100E nanobody complex in 2Up1Down… · 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 7Z9R · PDBe 7Z9R · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.