Research workbench

Caldalaklibacillus thermarum F1-ATPase (epsilon mutant)

Analyse Caldalaklibacillus thermarum F1-ATPase (epsilon mutant) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IK2
Type: protein
Length: 6,445 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase subunit alpha; ATP synthase subunit beta; ATP synthase gamma chain; ATP…
EC: 3.6.3.14
UniProt: F5LA74, F5LA72, F5LA73, F5LA71
Ligands: ADP, MG, PO4
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 10 distinct chains · 41% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, I	ATP synthase subunit alpha (EC 3.6.3.14)	protein	475	40% helix, 19% strand	F5LA74
B	ATP synthase subunit alpha (EC 3.6.3.14)	protein	469	39% helix, 21% strand	F5LA74
C	ATP synthase subunit alpha (EC 3.6.3.14)	protein	475	40% helix, 19% strand	F5LA74
D	ATP synthase subunit beta (EC 3.6.3.14)	protein	461	39% helix, 22% strand	F5LA72
E, F, L, M, N	ATP synthase subunit beta (EC 3.6.3.14)	protein	462	40% helix, 21% strand	F5LA72
G, O	ATP synthase gamma chain	protein	285	62% helix, 13% strand	F5LA73
H	ATP synthase epsilon chain	protein	132	29% helix, 45% strand	F5LA71
J	ATP synthase subunit alpha (EC 3.6.3.14)	protein	468	40% helix, 21% strand	F5LA74
K	ATP synthase subunit alpha (EC 3.6.3.14)	protein	476	39% helix, 20% strand	F5LA74
P	ATP synthase epsilon chain	protein	134	29% helix, 44% strand	F5LA71

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains A, D, B, E, C, F, I, L, J, M, K, N
MG · Magnesium ion · metal · 10 copies · chains A, B, C, D, F, I, J, K, L, N
PO4 · Phosphate ion · ion · 2 copies · chains A, E, I, M
GOL · Glycerol · additive · 16 copies · chains A, E, B, C, F, I, M, J, K, N

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	1128	0.88	0.90	146	ADP, MG
2	922	0.88	0.90	110	ADP, MG
3	918	0.87	0.89	101	ADP, MG
4	492	0.85	0.91	72	empty
5	544	0.84	0.90	63	ADP, MG

Interfaces

36 interfaces between chains.

K–L · 2967 Å² buried · 42 hydrogen bonds · protein-protein
C–D · 2836 Å² buried · 38 hydrogen bonds · protein-protein
A–D · 2260 Å² buried · 23 hydrogen bonds · protein-protein
I–L · 2231 Å² buried · 22 hydrogen bonds · protein-protein
B–F · 2222 Å² buried · 28 hydrogen bonds · protein-protein

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 F5LA74
Every structure of UniProt F5LA72
Every structure of UniProt F5LA73
Every structure of UniProt F5LA71
Elsewhere: RCSB PDB 5IK2 · PDBe 5IK2 · UniProt F5LA74 · UniProt F5LA72 · UniProt F5LA73 · UniProt F5LA71

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.