MolNFT v1 · #160660 · protein

E. COLI ATP synthase state 1E

6PQV · ATP synthase subunit delta: “E. COLI ATP synthase state 1E”. Electron microscopy, 4 ligands (ATP, ADP, MG), 20 pockets (best druggability 0.88). MolNFT v1 #160660 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6PQV
Type: protein
Length: 4,851 residues
Chains: 22
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase subunit delta; ATP synthase subunit alpha; ATP synthase subunit B; ATP…
EC: 7.1.2.2
UniProt: V0ZA15, A0A073FQ32, A0A073FPT7, A0A4V1DSB5, J7RYJ3, A0A0F6CB56, F4TL55, C3SL77
Ligands: ATP, ADP, MG, PO4
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 12 distinct chains · 49% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
W	ATP synthase subunit delta	protein	173	59% helix, 14% strand	V0ZA15
C	ATP synthase subunit alpha (EC 7.1.2.2)	protein	512	41% helix, 20% strand	A0A073FQ32
B	ATP synthase subunit alpha (EC 7.1.2.2)	protein	513	41% helix, 20% strand	A0A073FQ32
A	ATP synthase subunit alpha (EC 7.1.2.2)	protein	508	42% helix, 19% strand	A0A073FQ32
X, Y	ATP synthase subunit B	protein	156	87% helix, 0% strand	A0A073FPT7
H	ATP synthase epsilon chain	protein	136	23% helix, 40% strand	A0A4V1DSB5
G	ATP synthase gamma chain	protein	284	62% helix, 15% strand	J7RYJ3
F	ATP synthase subunit beta (EC 7.1.2.2)	protein	458	37% helix, 21% strand	A0A0F6CB56
E, D	ATP synthase subunit beta (EC 7.1.2.2)	protein	460	38% helix, 21% strand	A0A0F6CB56
J, L, M, N, O, P, Q, I, S	ATP synthase subunit C	protein	77	91% helix, 0% strand	F4TL55
R	ATP synthase subunit C	protein	76	93% helix, 0% strand	F4TL55
a	ATP synthase subunit a	protein	266	73% helix, 2% strand	C3SL77

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains C, F, B, E, A, D
ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains B, F, E, C, D
MG · Magnesium ion · metal · 5 copies · chains C, B, A, F, D
PO4 · Phosphate ion · ion · chains C, D

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	783	0.88	0.91	91	ATP, MG
2	1151	0.87	0.89	129	ATP, MG
3	914	0.86	0.88	107	ATP, MG
4	618	0.84	0.88	84	empty
5	899	0.83	0.85	91	ADP, MG

Interfaces

58 interfaces between chains.

X–Y · 2813 Å² buried · 15 hydrogen bonds · protein-protein
B–F · 2552 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 2477 Å² buried · 25 hydrogen bonds · protein-protein
H–G · 2461 Å² buried · 25 hydrogen bonds · protein-protein
C–F · 2358 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

6PQV · E. coli ATP Synthase State 1e · the same entry in another collection · chain W against W, 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 V0ZA15
Every structure of UniProt A0A073FQ32
Every structure of UniProt A0A073FPT7
Every structure of UniProt A0A4V1DSB5
Every structure of UniProt J7RYJ3
Every structure of UniProt A0A0F6CB56
Every structure of UniProt F4TL55
Every structure of UniProt C3SL77
Elsewhere: RCSB PDB 6PQV · PDBe 6PQV · UniProt V0ZA15 · UniProt A0A073FQ32 · UniProt A0A073FPT7 · UniProt A0A4V1DSB5 · UniProt J7RYJ3 · UniProt A0A0F6CB56 · UniProt F4TL55 · UniProt C3SL77

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