MolNFT v1 · #34979 · protein

Co-crystal structure analysis of GGA1-gae with the wnsf motif

2DWX · ADP-ribosylation factor-binding protein GGA1: “Co-crystal structure analysis of GGA1-gae with the wnsf motif”. X-ray diffraction, 8 pockets (best druggability 0.70). MolNFT v1 #34979 on GenesisL1: 3D structure, binding sites and…

PDB: 2DWX
Type: protein
Length: 520 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ADP-ribosylation factor-binding protein GGA1; Hinge peptide from ADP-ribosylation factor…
UniProt: Q9UJY5
Pockets: 8 · best druggability 0.70

Structure

x-ray diffraction · 5 distinct chains · 1% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	ADP-ribosylation factor-binding protein GGA1	protein	129	3% helix, 51% strand	Q9UJY5
B	ADP-ribosylation factor-binding protein GGA1	protein	119	0% helix, 39% strand	Q9UJY5
C	ADP-ribosylation factor-binding protein GGA1	protein	128	0% helix, 50% strand	Q9UJY5
P	Hinge peptide from ADP-ribosylation factor binding protein GGA1	protein	8	0% helix, 25% strand	Q9UJY5
Q	Hinge peptide from ADP-ribosylation factor binding protein GGA1	protein	7	0% helix, 29% strand	Q9UJY5

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	128	0.70	0.91	38	empty
2	207	0.58	0.80	32	empty
3	50	0.58	0.91	20	empty
4	75	0.56	0.87	22	empty
5	150	0.54	0.80	32	empty

Interfaces

9 interfaces between chains.

C–D · 1356 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1237 Å² buried · 6 hydrogen bonds · protein-protein
A–P · 637 Å² buried · 8 hydrogen bonds · protein-protein
C–Q · 594 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 247 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2DWX · Co-crystal Structure Analysis of GGA1-GAE with the WNSF motif · the same entry in another collection · chain Q against Q, TM-score 1.00
Q9UJY5 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-binding protein GGA1… · a predicted model of the same protein · chain C against A, TM-score 0.96

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 Q9UJY5
Elsewhere: RCSB PDB 2DWX · PDBe 2DWX · UniProt Q9UJY5

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