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Cryoem structure of polytomella F-ATP synthase, focussed refinement of upper peripheral stalk

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

PDB: 6RD6
Type: protein
Length: 1,035 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Asa-2: polytomella F-ATP synthase associated subunit 2; Mitochondrial ATP synthase…
UniProt: D7NIZ2, D8V7I2, D8V7I1, A0ZW40
Pockets: 12 · best druggability 0.73

Structure

electron microscopy · 5 distinct chains · 62% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	Asa-2: polytomella F-ATP synthase associated subunit 2	protein	441	67% helix, 6% strand	—
4	Mitochondrial ATP synthase associated protein ASA4	protein	290	71% helix, 1% strand	D7NIZ2
7	Mitochondrial ATP synthase associated protein ASA7	protein	176	51% helix, 14% strand	D8V7I2
P	Mitochondrial ATP synthase subunit oscp	protein	82	35% helix, 30% strand	D8V7I1
T	ATP synthase subunit alpha	protein	46	52% helix, 9% strand	A0ZW40

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	355	0.73	0.85	32	empty
2	341	0.72	0.84	37	empty
3	785	0.71	0.77	71	empty
4	489	0.68	0.79	60	empty
5	582	0.65	0.76	62	empty

Interfaces

9 interfaces between chains.

4–7 · 3094 Å² buried · 23 hydrogen bonds · protein-protein
2–7 · 2516 Å² buried · 36 hydrogen bonds · protein-protein
2–4 · 2137 Å² buried · 23 hydrogen bonds · protein-protein
4–T · 1647 Å² buried · 13 hydrogen bonds · protein-protein
P–T · 796 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6RD6 · CryoEM structure of Polytomella F-ATP synthase, focussed refinement of upper peripheral… · the same entry in another collection · chain 2 against 2, 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 D7NIZ2
Every structure of UniProt D8V7I2
Every structure of UniProt D8V7I1
Every structure of UniProt A0ZW40
Elsewhere: RCSB PDB 6RD6 · PDBe 6RD6 · UniProt D7NIZ2 · UniProt D8V7I2 · UniProt D8V7I1 · UniProt A0ZW40

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