Research workbench

Bovine F1-ATPase inhibited by dccd (dicyclohexylcarbodiimide)

Analyse Bovine F1-ATPase inhibited by dccd (dicyclohexylcarbodiimide) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1E79
Type: protein
Length: 3,316 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase alpha chain heart isoform; ATP synthase beta chain; ATP synthase gamma…
EC: 3.6.1.34
UniProt: P19483, P00829, P05631, P05630, P05632
Ligands: ADP, ATP, DCW, MG, SO4
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 6 distinct chains · 42% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	ATP synthase alpha chain heart isoform (EC 3.6.1.34)	protein	492	43% helix, 20% strand	P19483
D	ATP synthase beta chain (EC 3.6.1.34)	protein	467	38% helix, 20% strand	P00829
E, F	ATP synthase beta chain (EC 3.6.1.34)	protein	466	39% helix, 20% strand	P00829
G	ATP synthase gamma chain (EC 3.6.1.34)	protein	263	60% helix, 12% strand	P05631
H	ATP synthase delta chain (EC 3.6.1.34)	protein	131	27% helix, 39% strand	P05630
I	ATP synthase epsilon chain (EC 3.6.1.34)	protein	47	30% helix, 6% strand	P05632

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains B, E, C, D, F
ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, D, C, F
DCW · Dicyclohexylurea · ligand · chains D
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
SO4 · Sulfate ion · ion · chains A, E
GOL · Glycerol · additive · chains B

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	1198	0.87	0.89	112	ATP, MG
2	675	0.87	0.91	81	ATP, MG
3	654	0.84	0.88	71	empty
4	685	0.83	0.87	93	empty
5	365	0.83	0.92	51	empty

Interfaces

16 interfaces between chains.

C–D · 3067 Å² buried · 41 hydrogen bonds · protein-protein
A–D · 2570 Å² buried · 27 hydrogen bonds · protein-protein
C–F · 2344 Å² buried · 27 hydrogen bonds · protein-protein
B–F · 2131 Å² buried · 25 hydrogen bonds · protein-protein
B–E · 1979 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

1E79 · Bovine F1-ATPase inhibited by DCCD (dicyclohexylcarbodiimide) · 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 0.98
P05630 · AlphaFold monomer V2.0 prediction for ATP synthase subunit delta, mitochondrial (P05630) · a predicted model of the same protein · chain H against A, TM-score 0.98
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 1E79 · PDBe 1E79 · UniProt P19483 · UniProt P00829 · UniProt P05631 · UniProt P05630 · UniProt P05632

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