Research workbench
S protein of SARS-CoV-2 in complex bound with P5A-1B8_3B
Analyse S protein of SARS-CoV-2 in complex bound with P5A-1B8_3B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CZS
- Type
- protein
- Length
- 4,310 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.6
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein; IG c542_heavy_IGHV3-53_IGHD3-10_IGHJ6,IGH@ protein; IGL…
- UniProt
- P0DTC2, A0A5C2GG81, Q6GMX6, A0A5C2GCZ2, Q8TCD0
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 3.6 · 5 distinct chains · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1006 | 21% helix, 34% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1007 | 20% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1004 | 21% helix, 29% strand | P0DTC2 |
| H, I, J | IG c542_heavy_IGHV3-53_IGHD3-10_IGHJ6,IGH@ protein | protein | 217 | 4% helix, 44% strand | A0A5C2GG81, Q6GMX6 |
| K, M, N | IGL c4203_light_IGKV1-9_IGKJ4,Uncharacterized protein | protein | 214 | 5% helix, 38% strand | A0A5C2GCZ2, Q8TCD0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 71 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 | 1065 | 0.85 | 0.86 | 124 | empty |
| 2 | 590 | 0.82 | 0.87 | 65 | empty |
| 3 | 675 | 0.76 | 0.81 | 80 | empty |
| 4 | 701 | 0.75 | 0.80 | 47 | empty |
| 5 | 437 | 0.75 | 0.84 | 53 | empty |
Interfaces
14 interfaces between chains.
- B–C · 4221 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 4161 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 4138 Ų buried · 39 hydrogen bonds · protein-protein
- J–N · 1804 Ų buried · 8 hydrogen bonds · protein-protein
- H–K · 1796 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 49 disulfide, 48 glycan (disulfide, N-glycosylation).
Compared structures
- 7CZS · S protein of SARS-cov-2 in complex bound with P5A-1B8_3B · 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
- Every structure of UniProt A0A5C2GG81
- Every structure of UniProt Q6GMX6
- Every structure of UniProt A0A5C2GCZ2
- Every structure of UniProt Q8TCD0
- Elsewhere: RCSB PDB 7CZS · PDBe 7CZS · UniProt P0DTC2 · UniProt A0A5C2GG81 · UniProt Q6GMX6 · UniProt A0A5C2GCZ2 · UniProt Q8TCD0
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