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Cryoem structure of polytomella F-ATP synthase, primary rotary state 2, focussed refinement of F1 head and rotor

Analyse Cryoem structure of polytomella F-ATP synthase, primary rotary state 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RDE
Type: protein
Length: 4,502 residues
Chains: 20
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mitochondrial ATP synthase subunit C; Mitochondrial ATP synthase subunit oscp; Epsilon…
EC: 7.1.2.2
UniProt: D8V7I1, D7P7X6, Q4LDE7, A0ZW40, A0ZW41
Ligands: ATP, ADP, MG
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 11 distinct chains · 39% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	Mitochondrial ATP synthase subunit C	protein	74	88% helix, 0% strand	—
P	Mitochondrial ATP synthase subunit oscp	protein	113	67% helix, 0% strand	D8V7I1
Q	Epsilon: polytomella F-ATP synthase epsilon subunit	protein	72	36% helix, 13% strand	—
R	Mitochondrial ATP synthase subunit delta	protein	177	23% helix, 28% strand	D7P7X6
S	ATP synthase gamma chain, mitochondrial	protein	277	57% helix, 14% strand	Q4LDE7
T	ATP synthase subunit alpha	protein	483	39% helix, 20% strand	A0ZW40
U	ATP synthase subunit alpha	protein	523	38% helix, 20% strand	A0ZW40
V	ATP synthase subunit alpha	protein	520	38% helix, 19% strand	A0ZW40
X	ATP synthase subunit beta (EC 7.1.2.2)	protein	538	32% helix, 19% strand	A0ZW41
Y	ATP synthase subunit beta (EC 7.1.2.2)	protein	520	35% helix, 19% strand	A0ZW41
Z	ATP synthase subunit beta (EC 7.1.2.2)	protein	539	33% helix, 18% strand	A0ZW41

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains T, X, U, Z, V, Y
ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains T, Y, V, Z
MG · Magnesium ion · metal · 5 copies · chains T, U, V, Y, Z

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	618	0.85	0.90	84	empty
2	656	0.85	0.89	82	ATP, MG
3	500	0.84	0.91	66	empty
4	631	0.84	0.89	62	ATP, MG
5	1157	0.83	0.84	119	ADP, MG

Interfaces

50 interfaces between chains.

V–Z · 4053 Å² buried · 40 hydrogen bonds · protein-protein
U–X · 3638 Å² buried · 36 hydrogen bonds · protein-protein
T–Y · 3345 Å² buried · 33 hydrogen bonds · protein-protein
U–Z · 2623 Å² buried · 25 hydrogen bonds · protein-protein
V–Y · 2592 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6RDE · CryoEM structure of Polytomella F-ATP synthase, Primary rotary state 2, focussed… · the same entry in another collection · chain A against A, 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 D8V7I1
Every structure of UniProt D7P7X6
Every structure of UniProt Q4LDE7
Every structure of UniProt A0ZW40
Every structure of UniProt A0ZW41
Elsewhere: RCSB PDB 6RDE · PDBe 6RDE · UniProt D8V7I1 · UniProt D7P7X6 · UniProt Q4LDE7 · UniProt A0ZW40 · UniProt A0ZW41

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