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Structure of the yeast F1FO ATPase C10 ring with bound oligomycin

Analyse Structure of the yeast F1FO ATPase C10 ring with bound oligomycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4F4S
Type: protein
Length: 749 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase subunit 9, mitochondrial
UniProt: P61829
Ligands: EFO
Pockets: 4 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 91% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP synthase subunit 9, mitochondrial	protein	74	91% helix, 0% strand	P61829
B, C, D, E, K, L, M, N, O	ATP synthase subunit 9, mitochondrial	protein	75	91% helix, 0% strand	P61829

Ligands and binding sites

EFO · Oligomycin A · ligand · 7 copies · chains B, C, M, A, D, E, K, L, N, O

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	557	0.66	0.76	46	empty
2	170	0.42	0.73	21	empty
3	89	0.31	0.73	19	empty
4	60	0.26	0.72	14	empty

Interfaces

11 interfaces between chains.

M–N · 1563 Å² buried · 5 hydrogen bonds · protein-protein
K–L · 1556 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 1554 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 1537 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 1536 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (formylation).

Compared structures

4F4S · Structure of the yeast F1Fo ATPase c10 ring with bound oligomycin · the same entry in another collection · chain O against O, TM-score 1.00
P61829 · AlphaFold monomer V2.0 prediction for ATP synthase subunit 9, mitochondrial (P61829) · a predicted model of the same protein · chain E against A, TM-score 0.97

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 P61829
Elsewhere: RCSB PDB 4F4S · PDBe 4F4S · UniProt P61829

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