Research workbench

F1-ATPase in which all three catalytic sites contain bound nucleotide, with magnesium ion released in the empty site

Analyse F1-ATPase in which all three catalytic sites contain bound nucleotide, with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ASU
Type: protein
Length: 3,130 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase subunit alpha, mitochondrial; ATP synthase subunit beta, mitochondrial; ATP…
EC: 3.6.3.14
UniProt: P19483, P00829, P05631, P05630, P05632
Ligands: ADP, MG
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 9 distinct chains · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP synthase subunit alpha, mitochondrial	protein	487	42% helix, 20% strand	P19483
B	ATP synthase subunit alpha, mitochondrial	protein	480	41% helix, 20% strand	P19483
C	ATP synthase subunit alpha, mitochondrial	protein	485	42% helix, 19% strand	P19483
D	ATP synthase subunit beta, mitochondrial (EC 3.6.3.14)	protein	467	36% helix, 20% strand	P00829
E	ATP synthase subunit beta, mitochondrial (EC 3.6.3.14)	protein	458	35% helix, 20% strand	P00829
F	ATP synthase subunit beta, mitochondrial (EC 3.6.3.14)	protein	466	37% helix, 21% strand	P00829
G	ATP synthase subunit gamma, mitochondrial	protein	181	61% helix, 6% strand	P05631
H	ATP synthase subunit delta, mitochondrial	protein	83	0% helix, 55% strand	P05630
I	ATP synthase subunit epsilon, mitochondrial	protein	23	52% helix, 9% strand	P05632

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, D, B, E, C, F
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F

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	1043	0.89	0.91	133	empty
2	728	0.87	0.91	91	ADP, MG
3	771	0.84	0.88	72	ADP, MG
4	470	0.84	0.91	74	empty
5	501	0.84	0.90	65	empty

Interfaces

15 interfaces between chains.

C–D · 2641 Å² buried · 32 hydrogen bonds · protein-protein
A–D · 2567 Å² buried · 26 hydrogen bonds · protein-protein
C–F · 2452 Å² buried · 28 hydrogen bonds · protein-protein
B–F · 2297 Å² buried · 33 hydrogen bonds · protein-protein
B–E · 2013 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

4ASU · F1-ATPase in which all three catalytic sites contain bound nucleotide, with magnesium ion… · the same entry in another collection · chain I against I, TM-score 1.00
P19483 · AlphaFold monomer V2.0 prediction for ATP synthase subunit alpha, mitochondrial (P19483) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P19483
Every structure of UniProt P00829
Every structure of UniProt P05631
Every structure of UniProt P05630
Every structure of UniProt P05632
Elsewhere: RCSB PDB 4ASU · PDBe 4ASU · UniProt P19483 · UniProt P00829 · UniProt P05631 · UniProt P05630 · UniProt P05632

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.