Research workbench
Cryo-EM structure of Antibody 12-19 in complex with prefusion SARS-CoV-2 Spike glycoprotein
Analyse Cryo-EM structure of Antibody 12-19 in complex with prefusion SARS-CoV-2 Spike… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UKM
- Type
- protein
- Length
- 3,771 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.03
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein; 12-19 Fab Heavy Chain; 12-19 Fab Light Chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 3.03 · 3 distinct chains · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Spike glycoprotein | protein | 1012 | 23% helix, 32% strand | P0DTC2 |
| X, H, M | 12-19 Fab Heavy Chain | protein | 133 | 7% helix, 48% strand | — |
| Y, L, N | 12-19 Fab Light Chain | protein | 112 | 3% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 47 copies · chains B, C, A
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 | 867 | 0.87 | 0.90 | 116 | empty |
| 2 | 665 | 0.85 | 0.89 | 81 | empty |
| 3 | 1098 | 0.82 | 0.83 | 93 | empty |
| 4 | 755 | 0.81 | 0.85 | 80 | empty |
| 5 | 1102 | 0.80 | 0.81 | 110 | empty |
Interfaces
15 interfaces between chains.
- B–C · 4838 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 4837 Ų buried · 35 hydrogen bonds · protein-protein
- B–A · 4707 Ų buried · 36 hydrogen bonds · protein-protein
- H–L · 896 Ų buried · 14 hydrogen bonds · protein-protein
- M–N · 890 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 glycan, 45 disulfide (N-glycosylation, disulfide).
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 7UKM · PDBe 7UKM · UniProt P0DTC2
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