Research workbench
S protein of SARS-cov-2 in complex bound with P5A-3C12_1B
Analyse S protein of SARS-cov-2 in complex bound with P5A-3C12_1B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D0B
- Type
- protein
- Length
- 3,206 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain of P5A-3C12; Light chain of P5A-3C12
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 18% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1006 | 21% helix, 32% strand | P0DTC2 |
| B, C | Spike glycoprotein | protein | 981 | 19% helix, 31% strand | P0DTC2 |
| H | Heavy chain of P5A-3C12 | protein | 125 | 5% helix, 41% strand | — |
| L | Light chain of P5A-3C12 | protein | 113 | 0% helix, 32% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 69 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 | 1082 | 0.83 | 0.84 | 121 | empty |
| 2 | 766 | 0.82 | 0.86 | 95 | empty |
| 3 | 774 | 0.81 | 0.84 | 67 | empty |
| 4 | 824 | 0.80 | 0.83 | 91 | empty |
| 5 | 1049 | 0.80 | 0.81 | 90 | empty |
Interfaces
6 interfaces between chains.
- B–C · 4919 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 4630 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 4219 Ų buried · 28 hydrogen bonds · protein-protein
- H–L · 1044 Ų buried · 17 hydrogen bonds · protein-protein
- A–H · 418 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 48 glycan, 35 disulfide (N-glycosylation, disulfide).
Compared structures
- 7D0B · S protein of SARS-CoV-2 in complex bound with P5A-3C12_1B · 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 7D0B · PDBe 7D0B · UniProt P0DTC2
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