MolNFT v1 · #53238 · protein

ADP-ALF4 complex of S. cerevisiae GET3

2WOJ · ATPase GET3: “ADP-ALF4 complex of S. cerevisiae GET3”. X-ray diffraction, 4 ligands (ADP, ALF, MG), 20 pockets (best druggability 0.89). MolNFT v1 #53238 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2WOJ
Type: protein
Length: 1,190 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATPase GET3
EC: 3.6.3.16
UniProt: Q12154
Ligands: ADP, ALF, MG, ZN
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATPase GET3 (EC 3.6.3.16)	protein	301	51% helix, 15% strand	Q12154
B	ATPase GET3 (EC 3.6.3.16)	protein	301	51% helix, 15% strand	Q12154
C	ATPase GET3 (EC 3.6.3.16)	protein	284	50% helix, 16% strand	Q12154
D	ATPase GET3 (EC 3.6.3.16)	protein	304	51% helix, 14% strand	Q12154

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
ALF · Tetrafluoroaluminate ion · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 2 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	542	0.89	0.95	79	ADP, ALF, MG
2	551	0.88	0.94	79	ADP, ALF, MG
3	376	0.60	0.77	38	empty
4	246	0.55	0.77	32	empty
5	89	0.54	0.85	21	empty

Interfaces

3 interfaces between chains.

C–D · 2609 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 2582 Å² buried · 33 hydrogen bonds · protein-protein
A–D · 363 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2WOJ · ADP-AlF4 complex of S. cerevisiae GET3 · the same entry in another collection · chain D against D, TM-score 1.00
Q12154 · AlphaFold monomer V2.0 prediction for ATPase GET3 (Q12154) · 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 Q12154
Elsewhere: RCSB PDB 2WOJ · PDBe 2WOJ · UniProt Q12154

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