MolNFT v1 · #110437 · protein

Structure of GET3 bound to the transmembrane domain of SEC22

4XWO · ATPase GET3: “Structure of GET3 bound to the transmembrane domain of SEC22”. X-ray diffraction, 4 ligands (ADP, ATP, MG), 20 pockets (best druggability 0.89). MolNFT v1 #110437 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4XWO
Type: protein
Length: 5,938 residues
Chains: 28
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATPase GET3; Antibody heavy chain; Antibody light chain; SEC22
EC: 3.6.-.-
UniProt: Q12154
Ligands: ADP, ATP, MG, ZN
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 21 distinct chains · 32% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATPase GET3 (EC 3.6.-.-)	protein	293	49% helix, 15% strand	Q12154
B	ATPase GET3 (EC 3.6.-.-)	protein	297	51% helix, 14% strand	Q12154
C	Antibody heavy chain	protein	218	8% helix, 53% strand	—
D, P, R, X	Antibody light chain	protein	216	6% helix, 50% strand	—
E	Antibody heavy chain	protein	222	5% helix, 51% strand	—
F, J, L, V	Antibody light chain	protein	215	6% helix, 50% strand	—
G	ATPase GET3 (EC 3.6.-.-)	protein	294	51% helix, 16% strand	Q12154
H	ATPase GET3 (EC 3.6.-.-)	protein	300	50% helix, 15% strand	Q12154
I	Antibody heavy chain	protein	220	8% helix, 53% strand	—
K	Antibody heavy chain	protein	216	6% helix, 53% strand	—
M	ATPase GET3 (EC 3.6.-.-)	protein	304	51% helix, 14% strand	Q12154
N	ATPase GET3 (EC 3.6.-.-)	protein	300	50% helix, 15% strand	Q12154
O	Antibody heavy chain	protein	218	8% helix, 53% strand	—
Q, W	Antibody heavy chain	protein	221	7% helix, 52% strand	—
S	ATPase GET3 (EC 3.6.-.-)	protein	296	50% helix, 16% strand	Q12154
T	ATPase GET3 (EC 3.6.-.-)	protein	306	48% helix, 14% strand	Q12154
U	Antibody heavy chain	protein	214	8% helix, 50% strand	—
a	SEC22	protein	20	90% helix, 0% strand	—
g	SEC22	protein	14	86% helix, 0% strand	—
m	SEC22	protein	19	89% helix, 0% strand	—
s	SEC22	protein	21	90% helix, 0% strand	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, G, H, M, N, S, T
ATP · Adenosine-5'-triphosphate · ligand · 8 copies · chains A, B, G, H, M, N, S, T
MG · Magnesium ion · metal · 8 copies · chains A, B, G, H, M, N, S, T
ZN · Zinc ion · metal · 4 copies · chains A, B, G, H, M, N, S, T

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	666	0.89	0.93	79	MG, ADP, ATP
2	672	0.89	0.93	86	MG, ADP, ATP
3	621	0.88	0.94	82	MG, ADP, ATP
4	602	0.88	0.94	80	MG, ADP, ATP
5	973	0.79	0.80	100	empty

Interfaces

49 interfaces between chains.

M–N · 2674 Å² buried · 32 hydrogen bonds · protein-protein
G–H · 2651 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 2507 Å² buried · 35 hydrogen bonds · protein-protein
S–T · 2483 Å² buried · 29 hydrogen bonds · protein-protein
E–F · 1974 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 40 disulfide, 10 covalent (disulfide, covalent ligand).

Compared structures

4XWO · Structure of Get3 bound to the transmembrane domain of Sec22 · the same entry in another collection · chain B against B, TM-score 1.00

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 4XWO · PDBe 4XWO · UniProt Q12154

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