MolNFT v1 · #134457 · protein

Autoinhibited E. COLI ATP synthase state 1

5T4O · ATP synthase subunit alpha: “Autoinhibited E. COLI ATP synthase state 1”. Electron microscopy, 2 ligands (ATP, ADP), 20 pockets (best druggability 0.81). MolNFT v1 #134457 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5T4O
Type: protein
Length: 4,778 residues
Chains: 22
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase subunit alpha; ATP synthase subunit beta; ATP synthase gamma chain; ATP…
EC: 3.6.3.14
UniProt: B7MGF4, B7MGF2, B7MGF3, B7MGF1, P0ABA2, B7L888, B7MGF5, B7NR39
Ligands: ATP, ADP
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 10 distinct chains · 47% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP synthase subunit alpha (EC 3.6.3.14)	protein	511	39% helix, 10% strand	B7MGF4
B	ATP synthase subunit alpha (EC 3.6.3.14)	protein	510	35% helix, 10% strand	B7MGF4
C	ATP synthase subunit alpha (EC 3.6.3.14)	protein	508	37% helix, 10% strand	B7MGF4
D, E, F	ATP synthase subunit beta (EC 3.6.3.14)	protein	466	36% helix, 12% strand	B7MGF2
G	ATP synthase gamma chain	protein	284	60% helix, 7% strand	B7MGF3
H	ATP synthase epsilon chain	protein	136	22% helix, 29% strand	B7MGF1
I, J	ATP synthase subunit B	protein	155	89% helix, 0% strand	P0ABA2
K	ATP synthase subunit a	protein	211	82% helix, 0% strand	B7L888
L	ATP synthase subunit delta	protein	160	66% helix, 0% strand	B7MGF5
M, N, O, P, Q, R, S, T, U, V	ATP synthase subunit C	protein	75	96% helix, 0% strand	B7NR39

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, B, C
ADP · Adenosine-5'-diphosphate · ligand · chains B, 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	792	0.81	0.85	115	empty
2	820	0.81	0.84	122	empty
3	836	0.81	0.84	119	empty
4	981	0.78	0.81	118	empty
5	735	0.78	0.83	116	empty

Interfaces

37 interfaces between chains.

I–J · 952 Å² buried · 0 hydrogen bonds · protein-protein
M–V · 796 Å² buried · 2 hydrogen bonds · protein-protein
Q–R · 794 Å² buried · 2 hydrogen bonds · protein-protein
O–P · 792 Å² buried · 2 hydrogen bonds · protein-protein
R–S · 789 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

B7MGF4 · AlphaFold monomer V2.0 prediction for ATP synthase subunit alpha (B7MGF4) · a predicted model of the same protein · chain B against A, TM-score 0.93
B7MGF3 · AlphaFold monomer V2.0 prediction for ATP synthase gamma chain (B7MGF3) · a predicted model of the same protein · chain G against A, TM-score 0.89
B7NR39 · AlphaFold monomer V2.0 prediction for ATP synthase subunit C (B7NR39) · a predicted model of the same protein · chain V against A, TM-score 0.89

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 B7MGF4
Every structure of UniProt B7MGF2
Every structure of UniProt B7MGF3
Every structure of UniProt B7MGF1
Every structure of UniProt P0ABA2
Every structure of UniProt B7L888
Every structure of UniProt B7MGF5
Every structure of UniProt B7NR39
Elsewhere: RCSB PDB 5T4O · PDBe 5T4O · UniProt B7MGF4 · UniProt B7MGF2 · UniProt B7MGF3 · UniProt B7MGF1 · UniProt P0ABA2 · UniProt B7L888 · UniProt B7MGF5 · UniProt B7NR39

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