Research workbench

Bacillus PS3 ATP synthase class 3

Analyse Bacillus PS3 ATP synthase class 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6N30
Type: protein
Length: 4,711 residues
Chains: 22
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.2
Source: Bacillus sp. (strain PS3); Bacillus sp. PS3
Molecule: Bacillus PS3 ATP synthase subunit b; Bacillus PS3 ATP synthase subunit a; ATP synthase…
EC: 3.6.3.14
UniProt: P00845, A0A0M3VGF9, A0A0M4U1P9, A0A0M4TPJ7, A0A0M5MQR7
Ligands: ATP, ADP, MG, PO4
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · resolution 3.2 · 13 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
b2	Bacillus PS3 ATP synthase subunit b	protein	151	93% helix, 0% strand	—
b1	Bacillus PS3 ATP synthase subunit b	protein	157	95% helix, 0% strand	—
a	Bacillus PS3 ATP synthase subunit a	protein	203	73% helix, 0% strand	—
c3, c4, c5, c6, c7, c8, c9, c0, c1, c2	ATP synthase subunit c	protein	71	96% helix, 0% strand	P00845
C	ATP synthase subunit alpha (EC 3.6.3.14)	protein	494	39% helix, 17% strand	A0A0M3VGF9
A	ATP synthase subunit alpha (EC 3.6.3.14)	protein	500	37% helix, 20% strand	A0A0M3VGF9
B	ATP synthase subunit alpha (EC 3.6.3.14)	protein	499	39% helix, 19% strand	A0A0M3VGF9
F	ATP synthase subunit beta (EC 3.6.3.14)	protein	470	36% helix, 20% strand	A0A0M4U1P9
D	ATP synthase subunit beta (EC 3.6.3.14)	protein	469	37% helix, 19% strand	A0A0M4U1P9
E	ATP synthase subunit beta (EC 3.6.3.14)	protein	471	34% helix, 20% strand	A0A0M4U1P9
G	ATP synthase gamma chain	protein	284	58% helix, 11% strand	A0A0M4TPJ7
H	ATP synthase epsilon chain	protein	128	32% helix, 32% strand	A0A0M5MQR7
I	Bacillus PS3 ATP synthase subunit delta	protein	175	62% helix, 13% strand	—

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains C, F, A, D, B, E
ADP · Adenosine-5'-diphosphate · ligand · chains A, E
MG · Magnesium ion · metal · 4 copies · chains C, A, B, E
PO4 · Phosphate ion · ion · chains 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	988	0.88	0.89	103	ATP, MG
2	671	0.86	0.90	87	empty
3	322	0.84	0.94	59	empty
4	884	0.83	0.85	77	ATP, MG
5	1111	0.83	0.84	123	empty

Interfaces

55 interfaces between chains.

B–E · 2480 Å² buried · 18 hydrogen bonds · protein-protein
B–F · 2392 Å² buried · 23 hydrogen bonds · protein-protein
C–F · 2260 Å² buried · 23 hydrogen bonds · protein-protein
A–E · 2237 Å² buried · 23 hydrogen bonds · protein-protein
A–D · 2081 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent (covalent ligand).

Compared structures

P00845 · AlphaFold monomer V2.0 prediction for ATP synthase subunit C (P00845) · a predicted model of the same protein · chain c0 against A, TM-score 0.95

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 P00845
Every structure of UniProt A0A0M3VGF9
Every structure of UniProt A0A0M4U1P9
Every structure of UniProt A0A0M4TPJ7
Every structure of UniProt A0A0M5MQR7
Elsewhere: RCSB PDB 6N30 · PDBe 6N30 · UniProt P00845 · UniProt A0A0M3VGF9 · UniProt A0A0M4U1P9 · UniProt A0A0M4TPJ7 · UniProt A0A0M5MQR7

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