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Cryo-EM structure of polytomella F-ATP synthase, primary rotary state 2, monomer-masked refinement

Analyse Cryo-EM 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: 6RDD
Type: protein
Length: 2,597 residues
Chains: 13
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Asa-10: polytomella F-ATP synthase associated subunit 10; ATP synthase associated protein…
UniProt: Q85JD5, K0J903, D7NIZ2, A0A024FSR7, D7P897, D8V7I2, D8V7I7, H8PGG3, D8V7I1, A0ZW40
Ligands: ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 13 distinct chains · 58% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	Asa-10: polytomella F-ATP synthase associated subunit 10	protein	81	27% helix, 2% strand	—
1	ATP synthase associated protein ASA1	protein	595	61% helix, 1% strand	Q85JD5
2	Mitochondrial ATP synthase subunit ASA2	protein	441	58% helix, 5% strand	—
3	Mitochondrial F1F0 ATP synthase associated 32 kda protein	protein	245	65% helix, 2% strand	K0J903
4	Mitochondrial ATP synthase associated protein ASA4	protein	290	68% helix, 1% strand	D7NIZ2
5	Mitochondrial F1F0 ATP synthase associated 14 kda protein	protein	123	67% helix, 0% strand	A0A024FSR7
6	Mitochondrial ATP synthase subunit ASA6	protein	124	56% helix, 0% strand	D7P897
7	Mitochondrial ATP synthase associated protein ASA7	protein	176	44% helix, 13% strand	D8V7I2
8	Mitochondrial ATP synthase subunit ASA8	protein	88	57% helix, 0% strand	D8V7I7
9	Mitochondrial ATP synthase subunit ASA9	protein	97	45% helix, 0% strand	—
M	Mitochondrial ATP synthase subunit 6	protein	217	67% helix, 2% strand	H8PGG3
P	Mitochondrial ATP synthase subunit oscp	protein	80	33% helix, 23% strand	D8V7I1
T	ATP synthase subunit alpha	protein	40	40% helix, 0% strand	A0ZW40

Ligands and binding sites

ZN · Zinc ion · metal · chains 6, M

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1200	0.88	0.89	97	empty
2	919	0.82	0.83	84	empty
3	716	0.74	0.80	73	empty
4	827	0.73	0.78	68	empty
5	220	0.69	0.86	27	empty

Interfaces

41 interfaces between chains.

1–5 · 3921 Å² buried · 32 hydrogen bonds · protein-protein
4–7 · 3073 Å² buried · 27 hydrogen bonds · protein-protein
1–7 · 2758 Å² buried · 31 hydrogen bonds · protein-protein
2–7 · 2547 Å² buried · 34 hydrogen bonds · protein-protein
1–6 · 2294 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6RDD · Cryo-EM structure of Polytomella F-ATP synthase, Primary rotary state 2, monomer-masked… · the same entry in another collection · chain 0 against 0, 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 Q85JD5
Every structure of UniProt K0J903
Every structure of UniProt D7NIZ2
Every structure of UniProt A0A024FSR7
Every structure of UniProt D7P897
Every structure of UniProt D8V7I2
Every structure of UniProt D8V7I7
Every structure of UniProt H8PGG3
Every structure of UniProt D8V7I1
Every structure of UniProt A0ZW40
Elsewhere: RCSB PDB 6RDD · PDBe 6RDD · UniProt Q85JD5 · UniProt K0J903 · UniProt D7NIZ2 · UniProt A0A024FSR7 · UniProt D7P897 · UniProt D8V7I2 · UniProt D8V7I7 · UniProt H8PGG3 · UniProt D8V7I1 · UniProt A0ZW40

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