Research workbench
EM structure of SARS-cov-2 spike glycoprotein in complex with covox- 253H165L Fab
Analyse EM structure of SARS-cov-2 spike glycoprotein in complex with covox- 253H165L… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NDB
- Type
- protein
- Length
- 3,460 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Covox-253H165L Fab heavy chain; Covox-253H165L Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 993 | 24% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1031 | 23% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1003 | 25% helix, 31% strand | P0DTC2 |
| H | Covox-253H165L Fab heavy chain | protein | 219 | 9% helix, 50% strand | — |
| L | Covox-253H165L Fab light chain | protein | 214 | 7% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 49 copies · chains A, C, B, H
- FUC · alpha-L-fucopyranose · sugar · chains H
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 | 557 | 0.85 | 0.91 | 79 | empty |
| 2 | 1186 | 0.85 | 0.86 | 149 | empty |
| 3 | 733 | 0.84 | 0.87 | 84 | empty |
| 4 | 756 | 0.82 | 0.85 | 82 | empty |
| 5 | 350 | 0.79 | 0.89 | 41 | empty |
Interfaces
6 interfaces between chains.
- A–C · 5759 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 5551 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 4674 Ų buried · 35 hydrogen bonds · protein-protein
- H–L · 1786 Ų buried · 12 hydrogen bonds · protein-protein
- B–H · 457 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide, 38 glycan (disulfide, N-glycosylation).
Compared structures
- 7NDB · EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-253H165L Fab · 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 7NDB · PDBe 7NDB · UniProt P0DTC2
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