MolNFT v2 · #129912 · protein
CH3 chimera of human 14-3-3 sigma with the StARD1 peptide including Ser57
5OMA · 14-3-3 protein sigma,Steroidogenic acute regulatory…: “CH3 chimera of human 14-3-3 sigma with the StARD1 peptide including Ser57”. X-ray diffraction at 3.9, 2 ligands (PO4, SO4), 6 pockets (best druggability 0.67). MolNFT v2 #129912…
- PDB
- 5OMA
- Type
- protein
- Length
- 924 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.9
- Source
- Homo sapiens
- Molecule
- 14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial; Undetermined…
- UniProt
- P31947, P49675
- Ligands
- PO4, SO4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · resolution 3.9 · 5 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial | protein | 232 | 82% helix, 0% strand | P31947, P49675 |
| B | 14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial | protein | 236 | 81% helix, 0% strand | P31947, P49675 |
| C | 14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial | protein | 227 | 81% helix, 0% strand | P31947, P49675 |
| D | 14-3-3 protein sigma,Steroidogenic acute regulatory protein, mitochondrial | protein | 225 | 84% helix, 0% strand | P31947, P49675 |
| H | Undetermined peptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains C, H
- SO4 · Sulfate ion · ion · chains D
- 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
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.67 | 0.74 | 74 | empty |
| 2 | 247 | 0.56 | 0.78 | 26 | empty |
| 3 | 331 | 0.52 | 0.73 | 33 | PO4 |
| 4 | 291 | 0.51 | 0.74 | 33 | empty |
| 5 | 288 | 0.51 | 0.74 | 30 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1131 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1087 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 987 Ų buried · 15 hydrogen bonds · protein-protein
- C–H · 10 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5OMA · CH3 chimera of human 14-3-3 sigma with the STARD1 peptide including SER57 · 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 C against A, TM-score 0.98
- P49675 · AlphaFold monomer V2.0 prediction for steroidogenic acute regulatory protein… · a predicted model of the same protein · chain D against A, TM-score 0.31
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
- Every structure of UniProt P49675
- Elsewhere: RCSB PDB 5OMA · PDBe 5OMA · UniProt P31947 · UniProt P49675
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