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Structure of the F1C10 complex from yarrowia lipolytica ATP synthase

Analyse Structure of the F1C10 complex from yarrowia lipolytica ATP synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5FL7
Type: protein
Length: 3,996 residues
Chains: 19
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase subunit alpha; ATP synthase subunit beta; ATP synthase subunit gamma chain…
EC: 3.6.3.14, 3.6.1.34
UniProt: Q6C326, Q6CFT7, Q6C338, Q6C877, Q37695
Ligands: ATP, ADP, MG
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 13 distinct chains · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	ATP synthase subunit alpha	protein	485	35% helix, 20% strand	Q6C326
B	ATP synthase subunit alpha	protein	479	38% helix, 20% strand	Q6C326
D, F	ATP synthase subunit beta (EC 3.6.3.14)	protein	470	34% helix, 19% strand	Q6CFT7
E	ATP synthase subunit beta (EC 3.6.3.14)	protein	468	33% helix, 18% strand	Q6CFT7
G	ATP synthase subunit gamma chain, mitochondrial (EC 3.6.1.34)	protein	267	55% helix, 10% strand	Q6C338
H	ATP synthase delta chain, mitochondrial (EC 3.6.1.34)	protein	113	19% helix, 25% strand	Q6C877
I	ATP synthase epsilon chain, mitochondrial (EC 3.6.1.34)	protein	16	44% helix, 0% strand	—
K	ATP synthase subunit 9, mitochondrial (EC 3.6.3.14)	protein	73	93% helix, 0% strand	Q37695
L	ATP synthase subunit 9, mitochondrial (EC 3.6.3.14)	protein	72	96% helix, 0% strand	Q37695
M, O	ATP synthase subunit 9, mitochondrial (EC 3.6.3.14)	protein	75	96% helix, 0% strand	Q37695
N, P	ATP synthase subunit 9, mitochondrial (EC 3.6.3.14)	protein	75	87% helix, 0% strand	Q37695
Q	ATP synthase subunit 9, mitochondrial (EC 3.6.3.14)	protein	76	87% helix, 0% strand	Q37695
R, S, T	ATP synthase subunit 9, mitochondrial (EC 3.6.3.14)	protein	74	93% helix, 0% strand	Q37695

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, D, B, E, C, F
ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains C, D, B, 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	911	0.88	0.90	98	ATP, MG
2	937	0.87	0.89	119	empty
3	892	0.84	0.86	70	ATP, MG
4	897	0.83	0.85	72	ATP, MG
5	1173	0.83	0.84	108	ADP, MG

Interfaces

38 interfaces between chains.

A–D · 2652 Å² buried · 35 hydrogen bonds · protein-protein
C–F · 2604 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 2454 Å² buried · 30 hydrogen bonds · protein-protein
B–F · 2399 Å² buried · 32 hydrogen bonds · protein-protein
B–E · 2140 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

5FL7 · Structure of the F1c10 complex from Yarrowia lipolytica ATP synthase · the same entry in another collection · chain L against L, 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 Q6C326
Every structure of UniProt Q6CFT7
Every structure of UniProt Q6C338
Every structure of UniProt Q6C877
Every structure of UniProt Q37695
Elsewhere: RCSB PDB 5FL7 · PDBe 5FL7 · UniProt Q6C326 · UniProt Q6CFT7 · UniProt Q6C338 · UniProt Q6C877 · UniProt Q37695

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