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Bovine heart mitochondrial F1-ATPase inhibited by AMP-pnp and ADP in the presence of thiophosphate.

Analyse Bovine heart mitochondrial F1-ATPase inhibited by AMP-pnp and ADP in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YXW
Type: protein
Length: 3,236 residues
Chains: 9
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: P19483, P00829, P05631, P05630, P05632
Ligands: ANP, TS6, MG, NA, CL
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 9 distinct chains · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP synthase subunit alpha, mitochondrial	protein	489	41% helix, 20% strand	P19483
B	ATP synthase subunit alpha, mitochondrial	protein	480	39% helix, 20% strand	P19483
C	ATP synthase subunit alpha, mitochondrial	protein	488	41% helix, 19% strand	P19483
D	ATP synthase subunit beta, mitochondrial (EC 3.6.3.14)	protein	467	36% helix, 19% strand	P00829
E	ATP synthase subunit beta, mitochondrial (EC 3.6.3.14)	protein	458	35% helix, 20% strand	P00829
F	ATP synthase subunit beta, mitochondrial (EC 3.6.3.14)	protein	466	39% helix, 21% strand	P00829
G	ATP synthase subunit gamma, mitochondrial	protein	213	69% helix, 6% strand	P05631
H	ATP synthase subunit delta, mitochondrial	protein	128	30% helix, 32% strand	P05630
I	ATP synthase subunit epsilon, mitochondrial	protein	47	43% helix, 6% strand	P05632

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 5 copies · chains A, D, B, E, C, F
TS6 · Monothiophosphate · ligand · chains E
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
NA · Sodium ion · metal · chains F
CL · Chloride ion · ion · chains D

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	928	0.89	0.92	103	ANP, MG
2	1103	0.87	0.88	129	empty
3	535	0.84	0.90	69	empty
4	663	0.83	0.88	65	ANP, MG
5	1174	0.83	0.83	112	ANP, MG

Interfaces

16 interfaces between chains.

C–D · 3170 Å² buried · 44 hydrogen bonds · protein-protein
A–D · 2639 Å² buried · 32 hydrogen bonds · protein-protein
C–F · 2481 Å² buried · 25 hydrogen bonds · protein-protein
B–F · 2294 Å² buried · 28 hydrogen bonds · protein-protein
A–E · 2076 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

4YXW · Bovine heart mitochondrial F1-ATPase inhibited by AMP-PNP and ADP in the presence of… · the same entry in another collection · chain I against I, TM-score 1.00
P19483 · AlphaFold monomer V2.0 prediction for ATP synthase subunit alpha, mitochondrial (P19483) · a predicted model of the same protein · chain C against A, TM-score 0.99
P00829 · AlphaFold monomer V2.0 prediction for ATP synthase subunit beta, mitochondrial (P00829) · a predicted model of the same protein · chain E against A, TM-score 0.98

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
Elsewhere: RCSB PDB 4YXW · PDBe 4YXW · UniProt P19483 · UniProt P00829 · UniProt P05631 · UniProt P05630 · UniProt P05632

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