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Structure of human 14-3-3 gamma bound to O-glcnac peptide

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

PDB: 6BYJ
Type: protein
Length: 1,450 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 14-3-3 protein gamma; Tsttatppvsqasstttstw O-glcnac peptide
UniProt: P61981
Ligands: NAG
Pockets: 14 · best druggability 0.72

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	83% helix, 0% strand	P61981
B, C, D	14-3-3 protein gamma	protein	238	81% helix, 0% strand	P61981
E	14-3-3 protein gamma	protein	237	82% helix, 0% strand	P61981
F	14-3-3 protein gamma	protein	232	78% helix, 0% strand	P61981
G	Tsttatppvsqasstttstw O-glcnac peptide	protein	13	0% helix, 0% strand	—
P	Tsttatppvsqasstttstw O-glcnac peptide	protein	7	0% helix, 0% strand	—
T	Tsttatppvsqasstttstw O-glcnac peptide	protein	7	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

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	399	0.72	0.83	55	empty
2	667	0.68	0.77	67	empty
3	538	0.64	0.76	59	empty
4	307	0.54	0.75	25	empty
5	307	0.53	0.75	25	empty

Interfaces

9 interfaces between chains.

B–C · 1187 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 1146 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 1056 Å² buried · 9 hydrogen bonds · protein-protein
A–G · 894 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 758 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 glycan (O-glycosylation).

Compared structures

6BYJ · Structure of human 14-3-3 gamma bound to O-GlcNAc 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 6BYJ · PDBe 6BYJ · UniProt P61981

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