MolNFT v1 · #26506 · protein

Crystal structure of GGA3 gat domain in complex with ubiquitin

1WR6 · ADP-ribosylation factor binding protein GGA3: “Crystal structure of GGA3 gat domain in complex with ubiquitin”. X-ray diffraction, 10 pockets (best druggability 0.67). MolNFT v1 #26506 on GenesisL1: 3D structure, binding sites and…

PDB: 1WR6
Type: protein
Length: 649 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ADP-ribosylation factor binding protein GGA3; Ubiquitin
UniProt: Q9NZ52, P62990
Pockets: 10 · best druggability 0.67

Structure

x-ray diffraction · 7 distinct chains · 51% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ADP-ribosylation factor binding protein GGA3	protein	90	66% helix, 0% strand	Q9NZ52
B	ADP-ribosylation factor binding protein GGA3	protein	90	70% helix, 0% strand	Q9NZ52
C	ADP-ribosylation factor binding protein GGA3	protein	90	71% helix, 0% strand	Q9NZ52
D	ADP-ribosylation factor binding protein GGA3	protein	88	73% helix, 0% strand	Q9NZ52
E, G	Ubiquitin	protein	72	21% helix, 29% strand	P62990
F	Ubiquitin	protein	73	21% helix, 30% strand	P62990
H	Ubiquitin	protein	74	20% helix, 34% strand	P62990

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	257	0.67	0.83	28	empty
2	171	0.66	0.86	28	empty
3	223	0.50	0.76	26	empty
4	154	0.48	0.78	22	empty
5	97	0.39	0.76	18	empty

Interfaces

10 interfaces between chains.

B–C · 764 Å² buried · 9 hydrogen bonds · protein-protein
C–G · 716 Å² buried · 7 hydrogen bonds · protein-protein
B–F · 691 Å² buried · 8 hydrogen bonds · protein-protein
D–H · 687 Å² buried · 8 hydrogen bonds · protein-protein
A–E · 686 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

1WR6 · Crystal structure of GGA3 GAT domain in complex with ubiquitin · 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 B against A, TM-score 0.92

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 P62990
Elsewhere: RCSB PDB 1WR6 · PDBe 1WR6 · UniProt Q9NZ52 · UniProt P62990

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