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Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase

Analyse Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TJ5
Type: protein
Length: 2,467 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: V-type proton ATPase subunit a; V-type proton ATPase subunit C''; V-type proton ATPase…
UniProt: P32563, P23968, P32842, P25515, Q3E7B6, P32366
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 10 distinct chains · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	V-type proton ATPase subunit a	protein	570	67% helix, 0% strand	P32563
B	V-type proton ATPase subunit C''	protein	187	77% helix, 0% strand	P23968
D	V-type proton ATPase subunit C'	protein	147	78% helix, 0% strand	P32842
E	V-type proton ATPase subunit C	protein	138	83% helix, 0% strand	P25515
F, H, I, J	V-type proton ATPase subunit C	protein	150	80% helix, 0% strand	P25515
G	V-type proton ATPase subunit C	protein	149	81% helix, 0% strand	P25515
L	V-type proton ATPase subunit E	protein	57	51% helix, 0% strand	Q3E7B6
M, N	V-type proton ATPase subunit C	protein	148	81% helix, 0% strand	P25515
O	V-type proton ATPase subunit F	protein	54	80% helix, 0% strand	—
P	V-type proton ATPase subunit D	protein	269	65% helix, 0% strand	P32366

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	1127	0.80	0.82	110	empty
2	1104	0.77	0.79	97	empty
3	607	0.75	0.82	90	empty
4	524	0.73	0.82	79	empty
5	666	0.72	0.79	77	empty

Interfaces

22 interfaces between chains.

B–N · 1859 Å² buried · 5 hydrogen bonds · protein-protein
M–N · 1450 Å² buried · 2 hydrogen bonds · protein-protein
I–M · 1285 Å² buried · 1 hydrogen bond · protein-protein
F–G · 1233 Å² buried · 3 hydrogen bonds · protein-protein
G–H · 1196 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5TJ5 · Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase · the same entry in another collection · chain P against P, 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 P32563
Every structure of UniProt P23968
Every structure of UniProt P32842
Every structure of UniProt P25515
Every structure of UniProt Q3E7B6
Every structure of UniProt P32366
Elsewhere: RCSB PDB 5TJ5 · PDBe 5TJ5 · UniProt P32563 · UniProt P23968 · UniProt P32842 · UniProt P25515 · UniProt Q3E7B6 · UniProt P32366

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