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The structure of F1-ATPase from saccharomyces cerevisiae inhibited by its regulatory protein IF1

Analyse The structure of F1-ATPase from saccharomyces cerevisiae inhibited by its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZIA
Type: protein
Length: 6,676 residues
Chains: 20
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, P21306, P01097
Ligands: ADP, ATP, MG
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 9 distinct chains · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, K, M	ATP synthase subunit alpha, mitochondrial	protein	484	43% helix, 21% strand	P07251
B, L	ATP synthase subunit alpha, mitochondrial	protein	480	42% helix, 21% strand	P07251
D, N	ATP synthase subunit beta, mitochondrial (EC 3.6.3.14)	protein	470	37% helix, 21% strand	P00830
E, O	ATP synthase subunit beta, mitochondrial (EC 3.6.3.14)	protein	468	36% helix, 22% strand	P00830
F, P	ATP synthase subunit beta, mitochondrial (EC 3.6.3.14)	protein	469	38% helix, 22% strand	P00830
G, Q	ATP synthase subunit gamma, mitochondrial	protein	265	65% helix, 12% strand	P38077
H, R	ATP synthase subunit delta, mitochondrial	protein	124	27% helix, 37% strand	Q12165
I, S	ATP synthase subunit epsilon, mitochondrial	protein	58	38% helix, 16% strand	P21306
J, T	ATPase inhibitor, mitochondrial	protein	36	56% helix, 0% strand	P01097

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 10 copies · chains B, E, C, F, D, L, O, M, P, N
ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, D, K, N
MG · Magnesium ion · metal · 10 copies · chains A, B, C, D, F, K, L, M, N, P
EDO · 1,2-ethanediol · additive · 6 copies · chains C, L, P, M, O

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	1026	0.88	0.89	136	empty
2	674	0.85	0.90	105	empty
3	745	0.84	0.87	100	empty
4	664	0.84	0.89	70	ATP, MG
5	744	0.84	0.88	74	ATP, MG

Interfaces

47 interfaces between chains.

K–N · 2475 Å² buried · 34 hydrogen bonds · protein-protein
A–D · 2468 Å² buried · 37 hydrogen bonds · protein-protein
C–F · 2371 Å² buried · 29 hydrogen bonds · protein-protein
M–P · 2336 Å² buried · 26 hydrogen bonds · protein-protein
L–P · 2296 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

3ZIA · The structure of F1-ATPase from Saccharomyces cerevisiae inhibited by its regulatory… · the same entry in another collection · chain G against G, 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 P21306
Every structure of UniProt P01097
Elsewhere: RCSB PDB 3ZIA · PDBe 3ZIA · UniProt P07251 · UniProt P00830 · UniProt P38077 · UniProt Q12165 · UniProt P21306 · UniProt P01097

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