MolNFT v1 · #126040 · protein

Structure of F-ATPase from pichia angusta, in STATE2

5LQY · ATP synthase subunit F: “Structure of F-ATPase from pichia angusta, in STATE2”. Electron microscopy, 3 ligands (ADP, ATP, MG), 20 pockets (best druggability 0.84). MolNFT v1 #126040 on GenesisL1: 3D structure, binding sites and…

PDB: 5LQY
Type: protein
Length: 4,881 residues
Chains: 30
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase subunit F; ATP synthase subunit AAP1; ATP synthase subunit a; ATP synthase…
Ligands: ADP, ATP, MG
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 26 distinct chains · 44% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	ATP synthase subunit F	protein	30	93% helix, 0% strand	—
2	ATP synthase subunit AAP1	protein	25	92% helix, 0% strand	—
3	ATP synthase subunit a	protein	17	82% helix, 0% strand	—
4	ATP synthase subunit B	protein	27	89% helix, 0% strand	—
A	ATP synthase alpha subunit	protein	498	35% helix, 18% strand	—
B	ATP synthase alpha subunit	protein	498	34% helix, 19% strand	—
C	ATP synthase alpha subunit	protein	505	33% helix, 19% strand	—
D	ATP synthase beta subunit	protein	471	29% helix, 17% strand	—
E	ATP synthase beta subunit	protein	469	32% helix, 17% strand	—
F	ATP synthase beta subunit	protein	470	30% helix, 17% strand	—
G	ATP synthase gamma subunit	protein	267	57% helix, 10% strand	—
H	ATP synthase delta subunit	protein	128	26% helix, 27% strand	—
I	ATP synthase epsilon subunit	protein	57	30% helix, 21% strand	—
J	ATP synthase inhibitor protein IF1	protein	43	65% helix, 0% strand	—
K	ATP synthase C subunit	protein	73	84% helix, 0% strand	—
L	ATP synthase C subunit	protein	71	82% helix, 0% strand	—
M, N	ATP synthase C subunit	protein	72	78% helix, 0% strand	—
O, R, S	ATP synthase C subunit	protein	73	81% helix, 0% strand	—
P, Q	ATP synthase C subunit	protein	74	82% helix, 0% strand	—
T	ATP synthase C subunit	protein	72	78% helix, 0% strand	—
U	ATP synthase oscp subunit	protein	163	44% helix, 0% strand	—
V	ATP synthase subunit B	protein	154	94% helix, 0% strand	—
W	ATP synthase subunit D	protein	145	57% helix, 0% strand	—
X	ATP synthase subunit H	protein	21	43% helix, 0% strand	—
Y	ATP synthase subunit a	protein	122	71% helix, 0% strand	—
Z	ATP synthase subunit a	protein	44	68% helix, 0% strand	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains B, E, C, F, D
ATP · Adenosine-5'-triphosphate · ligand · chains A, D
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	1179	0.84	0.85	168	empty
2	1053	0.84	0.85	146	empty
3	603	0.82	0.87	117	empty
4	461	0.80	0.88	84	empty
5	580	0.79	0.86	93	empty

Interfaces

64 interfaces between chains.

C–F · 1057 Å² buried · 3 hydrogen bonds · protein-protein
V–W · 962 Å² buried · 1 hydrogen bond · protein-protein
A–D · 946 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 923 Å² buried · 6 hydrogen bonds · protein-protein
B–F · 919 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5LQY · Structure of F-ATPase from Pichia angusta, in state2 · the same entry in another collection · chain T against T, 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
Elsewhere: RCSB PDB 5LQY · PDBe 5LQY

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