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Structure of 14-3-3 gamma R57E mutant bound to glcnacylated peptide

Analyse Structure of 14-3-3 gamma R57E mutant bound to glcnacylated peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BZD
Type: protein
Length: 967 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 14-3-3 protein gamma; Glcnacylated peptide
UniProt: P61981
Ligands: NAG
Pockets: 5 · best druggability 0.53

Structure

x-ray diffraction · 4 distinct chains · 81% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	14-3-3 protein gamma	protein	238	83% helix, 0% strand	P61981
B, C	14-3-3 protein gamma	protein	237	83% helix, 0% strand	P61981
D	14-3-3 protein gamma	protein	233	81% helix, 0% strand	P61981
G, K	Glcnacylated peptide	protein	11	0% helix, 0% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, G, B, K

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	286	0.53	0.76	24	empty
2	273	0.51	0.75	24	empty
3	249	0.49	0.74	26	empty
4	209	0.49	0.75	26	empty
5	63	0.35	0.77	8	empty

Interfaces

6 interfaces between chains.

A–B · 1159 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1109 Å² buried · 15 hydrogen bonds · protein-protein
A–G · 745 Å² buried · 8 hydrogen bonds · protein-protein
B–K · 731 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 630 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6BZD · Structure of 14-3-3 gamma R57E mutant bound to GlcNAcylated peptide · the same entry in another collection · chain K against K, 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 A against A, TM-score 0.98

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 6BZD · PDBe 6BZD · UniProt P61981

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