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GGA3 vhs domain complexed with C-terminal peptide from cation- dependent mannose 6-phosphate receptor

Analyse GGA3 vhs domain complexed with C-terminal peptide from cation- dependent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JUQ
Type: protein
Length: 643 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ADP-ribosylation factor binding protein GGA3; Cation-dependent mannose-6-phosphate…
UniProt: Q9NZ52, P20645
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 6 distinct chains · 66% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ADP-ribosylation factor binding protein GGA3	protein	151	69% helix, 1% strand	Q9NZ52
E, G	Cation-dependent mannose-6-phosphate receptor	protein	5	0% helix, 0% strand	P20645
B, D	ADP-ribosylation factor binding protein GGA3	protein	159	70% helix, 1% strand	Q9NZ52
F	Cation-dependent mannose-6-phosphate receptor	protein	7	0% helix, 0% strand	P20645
C	ADP-ribosylation factor binding protein GGA3	protein	149	68% helix, 0% strand	Q9NZ52
H	Cation-dependent mannose-6-phosphate receptor	protein	8	0% helix, 0% strand	P20645

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1010	0.79	0.80	74	empty
2	999	0.77	0.79	75	empty
3	176	0.67	0.87	20	empty
4	131	0.63	0.86	24	empty
5	148	0.52	0.79	18	empty

Interfaces

9 interfaces between chains.

A–D · 852 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 776 Å² buried · 7 hydrogen bonds · protein-protein
B–F · 513 Å² buried · 9 hydrogen bonds · protein-protein
D–H · 499 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 389 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 modified (engineered).

Compared structures

1JUQ · GGA3 VHS domain complexed with C-terminal peptide from cation-dependent Mannose… · the same entry in another collection · chain H against H, TM-score 1.00
Q9NZ52 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-binding protein GGA3… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9NZ52
Every structure of UniProt P20645
Elsewhere: RCSB PDB 1JUQ · PDBe 1JUQ · UniProt Q9NZ52 · UniProt P20645

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