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Cryo-EM structure of polytomella F-ATP synthase, rotary substate 1E, focussed refinement of F1 head and rotor

Analyse Cryo-EM structure of polytomella F-ATP synthase, rotary substate 1E, focussed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RDV
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 · 38% 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	86% helix, 0% strand	—
P	Mitochondrial ATP synthase subunit oscp	protein	114	59% helix, 0% strand	D8V7I1
Q	Epsilon: polytomella F-ATP synthase epsilon subunit	protein	72	33% helix, 15% strand	—
R	Mitochondrial ATP synthase subunit delta	protein	177	25% helix, 27% strand	D7P7X6
S	ATP synthase gamma chain, mitochondrial	protein	277	57% helix, 14% strand	Q4LDE7
T	ATP synthase subunit alpha	protein	478	35% helix, 19% strand	A0ZW40
U	ATP synthase subunit alpha	protein	523	37% helix, 19% strand	A0ZW40
V	ATP synthase subunit alpha	protein	520	37% helix, 19% strand	A0ZW40
X	ATP synthase subunit beta (EC 7.1.2.2)	protein	542	32% helix, 18% strand	A0ZW41
Y	ATP synthase subunit beta (EC 7.1.2.2)	protein	521	35% helix, 17% strand	A0ZW41
Z	ATP synthase subunit beta (EC 7.1.2.2)	protein	538	32% 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 U, X, T, Y
MG · Magnesium ion · metal · 5 copies · chains T, U, V, X, Y

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	484	0.85	0.92	70	empty
2	1185	0.84	0.85	110	ATP, MG
3	420	0.84	0.92	63	ATP, MG
4	378	0.83	0.92	46	empty
5	386	0.83	0.91	51	empty

Interfaces

48 interfaces between chains.

U–X · 4079 Å² buried · 44 hydrogen bonds · protein-protein
V–Z · 3674 Å² buried · 38 hydrogen bonds · protein-protein
T–Y · 3500 Å² buried · 31 hydrogen bonds · protein-protein
V–Y · 2621 Å² buried · 27 hydrogen bonds · protein-protein
T–X · 2575 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

6RDV · Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1E, focussed refinement… · 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 6RDV · PDBe 6RDV · UniProt D8V7I1 · UniProt D7P7X6 · UniProt Q4LDE7 · UniProt A0ZW40 · UniProt A0ZW41

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