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Structure of 14-3-3 beta/alpha bound to O-ClcNAc peptide

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

PDB: 6BYK
Type: protein
Length: 948 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3
Source: Homo sapiens; SYNTHETIC CONSTRUCT
Molecule: 14-3-3 protein beta/alpha; ATPPVSQASSTT O-GlcNac peptide
UniProt: P31946
Ligands: NAG
Pockets: 13 · best druggability 0.65

Structure

x-ray diffraction · resolution 3 · 4 distinct chains · 75% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	14-3-3 protein beta/alpha	protein	230	81% helix, 0% strand	P31946
G, J	ATPPVSQASSTT O-GlcNac peptide	protein	9	0% helix, 0% strand	—
K	ATPPVSQASSTT O-GlcNac peptide	protein	5	0% helix, 0% strand	—
R	ATPPVSQASSTT O-GlcNac peptide	protein	5	0% helix, 0% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, G, D, J, A, K, C, R

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	649	0.65	0.75	44	empty
2	177	0.48	0.76	23	empty
3	73	0.44	0.81	22	NAG
4	96	0.43	0.79	24	NAG
5	67	0.40	0.80	18	empty

Interfaces

8 interfaces between chains.

C–D · 728 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 699 Å² buried · 6 hydrogen bonds · protein-protein
B–G · 696 Å² buried · 5 hydrogen bonds · protein-protein
D–J · 664 Å² buried · 6 hydrogen bonds · protein-protein
C–R · 396 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6BYK · Structure of 14-3-3 BETA/ALPHA bound to O-clcnac peptide · the same entry in another collection · chain R against R, TM-score 1.00
P31946 · AlphaFold monomer V2.0 prediction for 14-3-3 protein BETA/ALPHA (P31946) · a predicted model of the same protein · chain C 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 P31946
Elsewhere: RCSB PDB 6BYK · PDBe 6BYK · UniProt P31946

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