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Bovine ATP synthase F1-peripheral stalk domain, state 1

Analyse Bovine ATP synthase F1-peripheral stalk domain, state 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YY0
Type: protein
Length: 3,926 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase subunit alpha, mitochondrial; ATP synthase subunit beta, mitochondrial; ATP…
EC: 7.1.2.2
UniProt: P19483, P00829, P05631, P05630, P05632, P01096, P13621, P13619, P13620, P02721
Ligands: ATP, ADP, MG
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 13 distinct chains · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP synthase subunit alpha, mitochondrial	protein	508	40% helix, 20% strand	P19483
B	ATP synthase subunit alpha, mitochondrial	protein	477	40% helix, 19% strand	P19483
C	ATP synthase subunit alpha, mitochondrial	protein	498	41% helix, 19% strand	P19483
D	ATP synthase subunit beta, mitochondrial (EC 7.1.2.2)	protein	469	36% helix, 20% strand	P00829
E, F	ATP synthase subunit beta, mitochondrial (EC 7.1.2.2)	protein	467	38% helix, 19% strand	P00829
G	ATP synthase subunit gamma, mitochondrial	protein	272	62% helix, 15% strand	P05631
H	ATP synthase subunit delta, mitochondrial	protein	132	30% helix, 36% strand	P05630
I	ATP synthase subunit epsilon, mitochondrial	protein	47	53% helix, 9% strand	P05632
J	ATPase inhibitor, mitochondrial	protein	47	79% helix, 0% strand	P01096
S	ATP synthase subunit O, mitochondrial	protein	188	57% helix, 13% strand	P13621
b	ATP synthase F(0) complex subunit B1, mitochondrial	protein	136	91% helix, 0% strand	P13619
d	ATP synthase subunit D, mitochondrial	protein	156	57% helix, 0% strand	P13620
h	ATP synthase-coupling factor 6, mitochondrial	protein	62	56% helix, 0% strand	P02721

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, D, B, E, C, F
ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains C, D, E, 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	905	0.88	0.91	115	ATP, MG
2	682	0.87	0.91	78	ATP, MG
3	649	0.83	0.88	87	ADP, MG
4	731	0.83	0.87	81	ATP, MG
5	595	0.82	0.87	63	empty

Interfaces

35 interfaces between chains.

b–d · 3073 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 2555 Å² buried · 24 hydrogen bonds · protein-protein
C–F · 2293 Å² buried · 24 hydrogen bonds · protein-protein
B–F · 2166 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 2114 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

6YY0 · bovine ATP synthase F1-peripheral stalk domain, state 1 · the same entry in another collection · chain S against S, 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 P19483
Every structure of UniProt P00829
Every structure of UniProt P05631
Every structure of UniProt P05630
Every structure of UniProt P05632
Every structure of UniProt P01096
Every structure of UniProt P13621
Every structure of UniProt P13619
Every structure of UniProt P13620
Every structure of UniProt P02721
Elsewhere: RCSB PDB 6YY0 · PDBe 6YY0 · UniProt P19483 · UniProt P00829 · UniProt P05631 · UniProt P05630 · UniProt P05632 · UniProt P01096 · UniProt P13621 · UniProt P13619 · UniProt P13620 · UniProt P02721

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