MolNFT v1 · #103979 · protein

Crystal structure of an ATP-bound GET3-GET4-GET5 complex from S.CEREVISIAE

4PWX · ATPase GET3: “Crystal structure of an ATP-bound GET3-GET4-GET5 complex from S.CEREVISIAE”. X-ray diffraction, 3 ligands (ATP, MG, ZN), 15 pockets (best druggability 0.89). MolNFT v1 #103979 on GenesisL1: 3D structure, binding sites…

PDB: 4PWX
Type: protein
Length: 1,250 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATPase GET3; Golgi to er traffic protein 4; Ubiquitin-like protein MDY2
EC: 3.6.-.-
UniProt: Q12154, Q12125, Q12285
Ligands: ATP, MG, ZN
Pockets: 15 · best druggability 0.89

Structure

x-ray diffraction · 5 distinct chains · 59% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATPase GET3 (EC 3.6.-.-)	protein	294	48% helix, 14% strand	Q12154
B	ATPase GET3 (EC 3.6.-.-)	protein	299	49% helix, 14% strand	Q12154
E	Golgi to er traffic protein 4	protein	277	73% helix, 4% strand	Q12125
F, D	Ubiquitin-like protein MDY2	protein	52	25% helix, 0% strand	Q12285
C	Golgi to er traffic protein 4	protein	276	74% helix, 4% strand	Q12125

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
ZN · Zinc ion · metal · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	654	0.89	0.94	92	ATP, MG
2	1153	0.78	0.80	81	empty
3	1023	0.77	0.79	78	empty
4	92	0.57	0.86	17	empty
5	326	0.55	0.74	53	empty

Interfaces

7 interfaces between chains.

C–D · 2656 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 2643 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 2540 Å² buried · 30 hydrogen bonds · protein-protein
A–C · 478 Å² buried · 3 hydrogen bonds · protein-protein
B–E · 468 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4PWX · Crystal structure of an ATP-bound Get3-Get4-Get5 complex from S.cerevisiae · the same entry in another collection · chain D against D, TM-score 1.00
Q12125 · AlphaFold monomer V2.0 prediction for golgi to er traffic protein 4 (Q12125) · a predicted model of the same protein · chain C against A, TM-score 0.98
Q12154 · AlphaFold monomer V2.0 prediction for ATPase GET3 (Q12154) · a predicted model of the same protein · chain A against A, TM-score 0.95
Q12285 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein MDY2 (Q12285) · a predicted model of the same protein · chain F against A, TM-score 0.52

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
Every structure of UniProt Q12125
Every structure of UniProt Q12285
Elsewhere: RCSB PDB 4PWX · PDBe 4PWX · UniProt Q12154 · UniProt Q12125 · UniProt Q12285

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