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Structure of the E.COLI F1-ATP synthase inhibited by subunit epsilon

Analyse Structure of the E.COLI F1-ATP synthase inhibited by subunit epsilon in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3OAA
Type: protein
Length: 13,028 residues
Chains: 32
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: C9QXA2, C9QXA4, C9QXA3, C9QXA5
Ligands: ANP, ADP, MG, SO4
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 6 distinct chains · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, I, Q, Y	ATP synthase subunit alpha (EC 3.6.3.14)	protein	488	40% helix, 19% strand	C9QXA2
B, J, R, Z	ATP synthase subunit alpha (EC 3.6.3.14)	protein	486	37% helix, 18% strand	C9QXA2
C, K, S, a	ATP synthase subunit alpha (EC 3.6.3.14)	protein	487	38% helix, 19% strand	C9QXA2
D, E, F, L, M, N, T, U, V, b, c, d	ATP synthase subunit beta (EC 3.6.3.14)	protein	458	38% helix, 18% strand	C9QXA4
G, O, W, e	ATP synthase gamma chain	protein	284	62% helix, 14% strand	C9QXA3
H, P, X, f	ATP synthase epsilon chain	protein	138	26% helix, 41% strand	C9QXA5

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 12 copies · chains A, D, B, E, C, F, I, L, J, M, K, N, Q, T, R, U, S, V, Y, b, Z, c, a, d
ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains C, D, K, L, S, T, a, b
MG · Magnesium ion · metal · 16 copies · chains A, B, C, D, I, J, K, L, Q, R, S, T, Y, Z, a, b
SO4 · Sulfate ion · ion · 17 copies · chains C, D, A, E, B, F, G, H, K, L, I, M, J, N, O, P, S, T, Q, U, R, V, W, a, b, Y, c, Z, 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	1139	0.88	0.90	117	ANP, MG
2	819	0.88	0.91	105	ANP, MG
3	832	0.88	0.91	105	ANP, MG
4	1034	0.88	0.89	132	ANP, MG
5	762	0.88	0.91	88	ANP, MG

Interfaces

82 interfaces between chains.

S–T · 2610 Å² buried · 27 hydrogen bonds · protein-protein
K–L · 2575 Å² buried · 26 hydrogen bonds · protein-protein
B–F · 2566 Å² buried · 35 hydrogen bonds · protein-protein
e–f · 2560 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 2557 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

3OAA · Structure of the E.coli F1-ATP synthase inhibited by subunit Epsilon · the same entry in another collection · chain E against E, 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 C9QXA2
Every structure of UniProt C9QXA4
Every structure of UniProt C9QXA3
Every structure of UniProt C9QXA5
Elsewhere: RCSB PDB 3OAA · PDBe 3OAA · UniProt C9QXA2 · UniProt C9QXA4 · UniProt C9QXA3 · UniProt C9QXA5

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