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Yeast GLO3 gap domain

Analyse Yeast GLO3 gap domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JTZ
Type: protein
Length: 561 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ADP-ribosylation factor GTPase-activating protein GLO3
UniProt: P38682
Ligands: ZN
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 52% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	ADP-ribosylation factor GTPase-activating protein GLO3	protein	143	53% helix, 9% strand	P38682
A	ADP-ribosylation factor GTPase-activating protein GLO3	protein	139	53% helix, 8% strand	P38682
C	ADP-ribosylation factor GTPase-activating protein GLO3	protein	140	51% helix, 9% strand	P38682
D	ADP-ribosylation factor GTPase-activating protein GLO3	protein	139	51% helix, 9% strand	P38682

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains B, A, C, D
GOL · Glycerol · additive · 2 copies · chains B, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 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	576	0.71	0.80	51	empty
2	500	0.69	0.79	50	empty
3	347	0.64	0.79	44	empty
4	81	0.36	0.76	20	empty
5	54	0.33	0.77	16	empty

Interfaces

4 interfaces between chains.

B–A · 676 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 611 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 314 Å² buried · 1 hydrogen bond · protein-protein
B–C · 25 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7JTZ · Yeast Glo3 GAP domain · the same entry in another collection · chain D against D, TM-score 1.00
P38682 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor GTPase- activating protein… · a predicted model of the same protein · chain C 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 P38682
Elsewhere: RCSB PDB 7JTZ · PDBe 7JTZ · UniProt P38682

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