MolNFT v1 · #115546 · protein

Crystal structure of yeast GGA1_GAE domain-P21

5CN1 · ADP-ribosylation factor-binding protein GGA1: “Crystal structure of yeast GGA1_GAE domain-P21”. X-ray diffraction, 5 pockets (best druggability 0.69). MolNFT v1 #115546 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CN1
Type: protein
Length: 452 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ADP-ribosylation factor-binding protein GGA1
UniProt: Q06336
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 2% helix, 60% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	ADP-ribosylation factor-binding protein GGA1	protein	113	4% helix, 58% strand	Q06336
C	ADP-ribosylation factor-binding protein GGA1	protein	112	0% helix, 64% strand	Q06336
D	ADP-ribosylation factor-binding protein GGA1	protein	114	4% helix, 56% strand	Q06336

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	478	0.69	0.80	61	empty
2	329	0.62	0.79	43	empty
3	174	0.56	0.81	27	empty
4	185	0.52	0.78	25	empty
5	134	0.48	0.78	23	empty

Interfaces

6 interfaces between chains.

A–C · 758 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 698 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 403 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 401 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 330 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5CN1 · Crystal structure of yeast GGA1_GAE domain-P21 · the same entry in another collection · chain D against D, TM-score 1.00
Q06336 · 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 0.94

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 Q06336
Elsewhere: RCSB PDB 5CN1 · PDBe 5CN1 · UniProt Q06336

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