Research workbench
Fragment az-004 binding at a primary and secondary site in a P53PT387/14-3-3 complex
Analyse Fragment az-004 binding at a primary and secondary site in a P53PT387/14-3-3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S9Q
- Type
- protein
- Length
- 239 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14-3-3 protein sigma; Cellular tumor antigen P53
- UniProt
- P31947, P04637
- Ligands
- L1T, CA
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 14-3-3 protein sigma | protein | 227 | 83% helix, 0% strand | P31947 |
| P | Cellular tumor antigen P53 | protein | 12 | 0% helix, 0% strand | P04637 |
Ligands and binding sites
- L1T · 4-methyl-5-phenyl-thiophene-2-carboximidamide · ligand · 3 copies · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.38 | 0.78 | 17 | empty |
| 2 | 65 | 0.35 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–P · 823 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6S9Q · Fragment AZ-004 binding at a primary and secondary site in a p53pT387/14-3-3 complex · 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 0.96
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 P04637
- Elsewhere: RCSB PDB 6S9Q · PDBe 6S9Q · UniProt P31947 · UniProt P04637
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