Research workbench
Nanobody C5 bound to spike
Analyse Nanobody C5 bound to spike in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OAN
- Type
- protein
- Length
- 3,510 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Immunoglobulin mu heavy chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1049 | 21% helix, 33% strand | P0DTC2 |
| F, G, H | Immunoglobulin mu heavy chain | protein | 121 | 2% 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 | 988 | 0.83 | 0.84 | 86 | empty |
| 2 | 993 | 0.82 | 0.83 | 94 | empty |
| 3 | 546 | 0.81 | 0.87 | 42 | empty |
| 4 | 537 | 0.80 | 0.86 | 79 | empty |
| 5 | 780 | 0.79 | 0.83 | 64 | empty |
Interfaces
9 interfaces between chains.
- B–C · 4846 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 4844 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 4827 Ų buried · 46 hydrogen bonds · protein-protein
- B–G · 831 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 830 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 glycan, 48 disulfide (N-glycosylation, disulfide).
Compared structures
- 7OAN · Nanobody C5 bound to Spike · 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 7OAN · PDBe 7OAN · UniProt P0DTC2
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