Research workbench
SARS-cov-2 nucleocapsid phosphopeptide 193-200 bound to human 14-3-3 sigma
Analyse SARS-cov-2 nucleocapsid phosphopeptide 193-200 bound to human 14-3-3 sigma in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QIK
- Type
- protein
- Length
- 461 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14-3-3 protein sigma; Ser-ser-arg-asn-sep-thr-pro-gly
- UniProt
- P31947
- Ligands
- BR
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 14-3-3 protein sigma | protein | 222 | 83% helix, 0% strand | P31947 |
| B | 14-3-3 protein sigma | protein | 225 | 83% helix, 0% strand | P31947 |
| E | Ser-ser-arg-asn-sep-thr-pro-gly | protein | 8 | 0% helix, 0% strand | — |
| F | Ser-ser-arg-asn-sep-thr-pro-gly | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- BR · Bromide ion · ion · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.58 | 0.80 | 26 | empty |
| 2 | 335 | 0.56 | 0.75 | 22 | PEG |
| 3 | 178 | 0.54 | 0.79 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1050 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 519 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 470 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 7QIK · SARS-CoV-2 Nucleocapsid phosphopeptide 193-200 bound to human 14-3-3 sigma · the same entry in another collection · chain A against A, TM-score 1.00
- P31947 · AlphaFold monomer V2.0 prediction for 14-3-3 protein sigma (P31947) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P31947
- Elsewhere: RCSB PDB 7QIK · PDBe 7QIK · UniProt P31947
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