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Structure of 14-3-3 gamma bound to O-glcnacylated thr peptide

Analyse Structure of 14-3-3 gamma bound to O-glcnacylated thr peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BYL
Type: protein
Length: 1,447 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 14-3-3 protein gamma; Tsasttvpvttatttttstw O-glcnac peptide
UniProt: P61981
Ligands: NAG
Pockets: 16 · best druggability 0.67

Structure

x-ray diffraction · 7 distinct chains · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	14-3-3 protein gamma	protein	240	81% helix, 0% strand	P61981
B, E	14-3-3 protein gamma	protein	237	81% helix, 0% strand	P61981
C, D	14-3-3 protein gamma	protein	238	82% helix, 0% strand	P61981
F	14-3-3 protein gamma	protein	232	75% helix, 0% strand	P61981
G	Tsasttvpvttatttttstw O-glcnac peptide	protein	13	0% helix, 0% strand	—
P	Tsasttvpvttatttttstw O-glcnac peptide	protein	7	0% helix, 0% strand	—
T	Tsasttvpvttatttttstw O-glcnac peptide	protein	5	0% helix, 0% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, G, D, P, C, T

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

Pockets

16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	570	0.67	0.77	59	empty
2	373	0.66	0.80	44	empty
3	561	0.65	0.76	55	empty
4	317	0.54	0.75	25	empty
5	258	0.53	0.76	26	empty

Interfaces

9 interfaces between chains.

B–C · 1184 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 1149 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 1045 Å² buried · 7 hydrogen bonds · protein-protein
A–G · 893 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 765 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan (O-glycosylation, glycosylation).

Compared structures

6BYL · Structure of 14-3-3 gamma bound to O-GlcNAcylated thr peptide · the same entry in another collection · chain T against T, TM-score 1.00
P61981 · AlphaFold monomer V2.0 prediction for 14-3-3 protein gamma (P61981) · a predicted model of the same protein · chain D 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 P61981
Elsewhere: RCSB PDB 6BYL · PDBe 6BYL · UniProt P61981

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