Research workbench
SARS-cov-2 spike protein in complex with a pan-sarbecovirus nanobody 2-34
Analyse SARS-cov-2 spike protein in complex with a pan-sarbecovirus nanobody 2-34 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CY7
- Type
- protein
- Length
- 3,513 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Pan-sarbecovirus nanobody 2-38
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1050 | 22% helix, 26% strand | P0DTC2 |
| D, E, F | Pan-sarbecovirus nanobody 2-38 | protein | 121 | 2% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 74 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 | 1046 | 0.86 | 0.87 | 130 | empty |
| 2 | 687 | 0.84 | 0.88 | 72 | empty |
| 3 | 851 | 0.82 | 0.84 | 70 | empty |
| 4 | 990 | 0.81 | 0.82 | 93 | empty |
| 5 | 1027 | 0.79 | 0.80 | 81 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4396 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 4236 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 4119 Ų buried · 21 hydrogen bonds · protein-protein
- B–E · 787 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 641 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide, 38 glycan (disulfide, N-glycosylation).
Compared structures
- 8CY7 · SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-34 · the same entry in another collection · chain C against C, 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 8CY7 · PDBe 8CY7 · UniProt P0DTC2
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