MolNFT v1 · #162814 · protein

Fragment az-015 binding at the P53PT387/14-3-3 sigma interface

6RJZ · 14-3-3 protein sigma: “Fragment az-015 binding at the P53PT387/14-3-3 sigma interface”. X-ray diffraction, 3 ligands (K6B, MG, CL), 3 pockets (best druggability 0.48). MolNFT v1 #162814 on GenesisL1: 3D structure, binding sites and…

PDB: 6RJZ
Type: protein
Length: 240 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: K6B, MG, CL
Pockets: 3 · best druggability 0.48

Structure

x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	14-3-3 protein sigma	protein	228	82% helix, 0% strand	P31947
P	Cellular tumor antigen P53	protein	12	0% helix, 0% strand	P04637

Ligands and binding sites

K6B · 7-(6-azanylpyridin-2-yl)-1-benzothiophene-2-carboximidamide · ligand · chains A
MG · Magnesium ion · metal · 2 copies · chains A
CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	114	0.48	0.79	25	empty
2	77	0.37	0.77	15	empty
3	50	0.33	0.78	16	empty

Interfaces

1 interface between chains.

A–P · 837 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (oxidation, phosphorylation).

Compared structures

6RJZ · Fragment AZ-015 binding at the p53pT387/14-3-3 sigma interface · 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 6RJZ · PDBe 6RJZ · UniProt P31947 · UniProt P04637

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