MolNFT v1 · #162601 · protein

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

6RDY · Mitochondrial ATP synthase subunit C: “Cryo-EM structure of polytomella F-ATP synthase, rotary substate 1F, focussed refinement of F1 head and rotor”. Electron microscopy, 3 ligands (ATP, ADP, MG), 20 pockets (best druggability…

PDB: 6RDY
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: D7P7X5, D8V7I1, D7P7X6, Q4LDE7, A0ZW40, A0ZW41
Ligands: ATP, ADP, MG
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 11 distinct chains · 37% helix, 17% 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	91% helix, 0% strand	D7P7X5
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, 10% strand	—
R	Mitochondrial ATP synthase subunit delta	protein	177	27% helix, 28% strand	D7P7X6
S	ATP synthase gamma chain, mitochondrial	protein	277	52% helix, 15% strand	Q4LDE7
T	ATP synthase subunit alpha	protein	478	35% helix, 20% strand	A0ZW40
U	ATP synthase subunit alpha	protein	523	37% helix, 18% strand	A0ZW40
V	ATP synthase subunit alpha	protein	520	35% helix, 18% strand	A0ZW40
X	ATP synthase subunit beta (EC 7.1.2.2)	protein	542	33% helix, 18% strand	A0ZW41
Y	ATP synthase subunit beta (EC 7.1.2.2)	protein	521	33% helix, 17% strand	A0ZW41
Z	ATP synthase subunit beta (EC 7.1.2.2)	protein	538	30% helix, 17% 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	791	0.84	0.87	89	ATP, MG
2	634	0.84	0.88	76	ATP, MG
3	811	0.84	0.86	77	ADP, MG
4	387	0.84	0.92	53	empty
5	399	0.82	0.91	47	empty

Interfaces

48 interfaces between chains.

U–X · 4138 Å² buried · 50 hydrogen bonds · protein-protein
V–Z · 3754 Å² buried · 32 hydrogen bonds · protein-protein
T–Y · 3480 Å² buried · 35 hydrogen bonds · protein-protein
V–Y · 2702 Å² buried · 28 hydrogen bonds · protein-protein
T–X · 2677 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

6RDY · Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1F, 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 D7P7X5
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 6RDY · PDBe 6RDY · UniProt D7P7X5 · UniProt D8V7I1 · UniProt D7P7X6 · UniProt Q4LDE7 · UniProt A0ZW40 · UniProt A0ZW41

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