Research workbench
Cryoem structure of DEL68-76/DEL679-688 prefusion-stabilized spike in complex with the Fab of N12-9
Analyse Cryoem structure of DEL68-76/DEL679-688 prefusion-stabilized spike in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V23
- Type
- protein
- Length
- 3,774 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; The heavy chain of N12-9 Fab; The light chain of N12-9 Fab
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1018 | 22% helix, 32% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1038 | 21% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1031 | 22% helix, 32% strand | P0DTC2 |
| O, Q, S | The heavy chain of N12-9 Fab | protein | 124 | 10% helix, 40% strand | — |
| P, R, T | The light chain of N12-9 Fab | protein | 105 | 6% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 48 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 | 750 | 0.86 | 0.90 | 96 | empty |
| 2 | 1153 | 0.84 | 0.85 | 118 | empty |
| 3 | 793 | 0.82 | 0.85 | 82 | empty |
| 4 | 1029 | 0.82 | 0.83 | 108 | empty |
| 5 | 589 | 0.76 | 0.83 | 41 | empty |
Interfaces
12 interfaces between chains.
- B–C · 4595 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 4452 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 4401 Ų buried · 37 hydrogen bonds · protein-protein
- O–P · 857 Ų buried · 2 hydrogen bonds · protein-protein
- Q–R · 847 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 32 glycan (disulfide, N-glycosylation).
Compared structures
- 7V23 · CryoEM structure of del68-76/del679-688 prefusion-stabilized spike in complex with the… · 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 7V23 · PDBe 7V23 · UniProt P0DTC2
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