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Rotor architecture in the F(1)-C(10)-ring complex of the yeast F-ATP synthase

Analyse Rotor architecture in the F(1)-C(10)-ring complex of the yeast F-ATP synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZRY
Type: protein
Length: 4,014 residues
Chains: 19
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase subunit alpha, mitochondrial; ATP synthase subunit beta, mitochondrial; ATP…
EC: 3.6.3.14
UniProt: P07251, P00830, P38077, Q12165, E9P9X4, P61829
Ligands: ANP, MG
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 15 distinct chains · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP synthase subunit alpha, mitochondrial	protein	482	41% helix, 23% strand	P07251
B	ATP synthase subunit alpha, mitochondrial	protein	483	37% helix, 20% strand	P07251
C	ATP synthase subunit alpha, mitochondrial	protein	484	40% helix, 20% strand	P07251
D	ATP synthase subunit beta, mitochondrial (EC 3.6.3.14)	protein	470	38% helix, 21% strand	P00830
E	ATP synthase subunit beta, mitochondrial (EC 3.6.3.14)	protein	468	37% helix, 20% strand	P00830
F	ATP synthase subunit beta, mitochondrial (EC 3.6.3.14)	protein	469	37% helix, 21% strand	P00830
G	ATP synthase subunit gamma, mitochondrial	protein	265	58% helix, 12% strand	P38077
H	ATP synthase subunit delta, mitochondrial (EC 3.6.3.14)	protein	119	24% helix, 24% strand	Q12165
I	ATP synthase catalytic sector F1 epsilon subunit	protein	48	19% helix, 13% strand	E9P9X4
J	ATP synthase subunit 9, mitochondrial	protein	72	89% helix, 0% strand	P61829
K	ATP synthase subunit 9, mitochondrial	protein	72	83% helix, 0% strand	P61829
L	ATP synthase subunit 9, mitochondrial	protein	71	90% helix, 0% strand	P61829
M, N	ATP synthase subunit 9, mitochondrial	protein	72	83% helix, 0% strand	P61829
O, R, S	ATP synthase subunit 9, mitochondrial	protein	73	89% helix, 0% strand	P61829
P, Q	ATP synthase subunit 9, mitochondrial	protein	74	88% helix, 0% strand	P61829

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 5 copies · chains A, D, B, E, C, F
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F

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	622	0.86	0.91	79	ANP, MG
2	1036	0.84	0.85	107	ANP, MG
3	917	0.83	0.84	96	ANP, MG
4	568	0.83	0.88	51	ANP, MG
5	589	0.82	0.88	52	empty

Interfaces

37 interfaces between chains.

A–D · 2421 Å² buried · 36 hydrogen bonds · protein-protein
B–F · 2400 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 2323 Å² buried · 28 hydrogen bonds · protein-protein
C–F · 2165 Å² buried · 17 hydrogen bonds · protein-protein
A–E · 2012 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

3ZRY · Rotor architecture in the F(1)-c(10)-ring complex of the yeast F-ATP synthase · the same entry in another collection · chain K against K, 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 P07251
Every structure of UniProt P00830
Every structure of UniProt P38077
Every structure of UniProt Q12165
Every structure of UniProt E9P9X4
Every structure of UniProt P61829
Elsewhere: RCSB PDB 3ZRY · PDBe 3ZRY · UniProt P07251 · UniProt P00830 · UniProt P38077 · UniProt Q12165 · UniProt E9P9X4 · UniProt P61829

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