Research workbench
CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-H4 Q98R H100E nanobody complex in 1Up2Down 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
- 7Z86
- Type
- protein
- Length
- 3,348 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.4
- Source
- Escherichia virus T4; Lama glama; Severe acute respiratory syndrome coronavirus…
- Molecule
- Spike glycoprotein,Fibritin; Nanobody H11-H4 Q98R H100E
- UniProt
- P0DTC2, P10104
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 3.4 · 4 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein,Fibritin | protein | 987 | 22% helix, 33% strand | P0DTC2, P10104 |
| B | Spike glycoprotein,Fibritin | protein | 992 | 23% helix, 32% strand | P0DTC2, P10104 |
| C | Spike glycoprotein,Fibritin | protein | 991 | 23% helix, 33% strand | P0DTC2, P10104 |
| X, Y, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.86 | 0.87 | 121 | empty |
| 2 | 722 | 0.85 | 0.89 | 78 | empty |
| 3 | 856 | 0.83 | 0.85 | 86 | empty |
| 4 | 562 | 0.81 | 0.87 | 79 | empty |
| 5 | 1133 | 0.79 | 0.81 | 104 | empty |
Interfaces
7 interfaces between chains.
- B–C · 4891 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 4764 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 4522 Ų buried · 36 hydrogen bonds · protein-protein
- A–X · 701 Ų buried · 9 hydrogen bonds · protein-protein
- B–Y · 689 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 7Z86 · Cryo-EM structure of SARS-cov-2 spike : H11-H4 Q98R H100E nanobody complex in 1UP2DOWN… · 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
- Every structure of UniProt P10104
- Elsewhere: RCSB PDB 7Z86 · PDBe 7Z86 · UniProt P0DTC2 · UniProt P10104
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