Research workbench
Structure of the SARS-cov-2 ntd in complex with C1520, local refinement
Analyse Structure of the SARS-cov-2 ntd in complex with C1520, local refinement in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UAQ
- Type
- protein
- Length
- 533 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; C1520 Fab heavy chain; C1520 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.69
Structure
electron microscopy · 3 distinct chains · 3% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 295 | 3% helix, 37% strand | P0DTC2 |
| H | C1520 Fab heavy chain | protein | 126 | 2% helix, 37% strand | — |
| L | C1520 Fab light chain | protein | 112 | 5% helix, 34% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.69 | 0.95 | 25 | empty |
| 2 | 235 | 0.61 | 0.81 | 33 | empty |
| 3 | 75 | 0.52 | 0.85 | 25 | empty |
| 4 | 122 | 0.52 | 0.81 | 23 | empty |
| 5 | 180 | 0.46 | 0.75 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–H · 949 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 926 Ų buried · 11 hydrogen bonds · protein-protein
- A–L · 236 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 7UAQ · Structure of the SARS-CoV-2 NTD in complex with C1520, local refinement · 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 7UAQ · PDBe 7UAQ · UniProt P0DTC2
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