Research workbench

Fo domain of ovine ATP synthase

Analyse Fo domain of ovine ATP synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZA9
Type: protein
Length: 1,374 residues
Chains: 17
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase F(0) complex subunit C1, mitochondrial; ATP synthase subunit B; ATP synthase…
UniProt: P17605, W5QEA9, W5PP37, O78752, W5P5H1, W5P913, O78751, W5QB48, W5Q5U7, W5PF18
Ligands: LHG, CDL, S12
Pockets: 16 · best druggability 0.90

Structure

electron microscopy · 10 distinct chains · 71% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1, 2, 3, 4, 5, 6, 7, 8	ATP synthase F(0) complex subunit C1, mitochondrial	protein	74	86% helix, 0% strand	P17605
K	ATP synthase subunit B	protein	119	71% helix, 2% strand	W5QEA9
M	ATP synthase subunit D, mitochondrial	protein	60	52% helix, 2% strand	W5PP37
N	ATP synthase subunit a	protein	225	73% helix, 0% strand	O78752
O	ATP synthase membrane subunit dapit	protein	40	63% helix, 0% strand	W5P5H1
P	ATP synthase membrane subunit 6.8PL	protein	52	83% helix, 0% strand	W5P913
Q	ATP synthase protein 8	protein	47	51% helix, 0% strand	O78751
R	ATP synthase membrane subunit F	protein	84	64% helix, 1% strand	W5QB48
S	ATP synthase subunit	protein	85	71% helix, 1% strand	W5Q5U7
T	ATP synthase subunit E, mitochondrial	protein	70	87% helix, 0% strand	W5PF18

Ligands and binding sites

LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 6 copies · chains 2, N, P, Q, K, S, T, R
CDL · Cardiolipin · ligand · 3 copies · chains N, P, Q, R, K, S
S12 · O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine · ligand · chains 1, 2, 3, 4, 5, 6, 7, 8, T

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1012	0.90	0.92	104	S12
2	962	0.77	0.79	75	CDL
3	377	0.73	0.84	49	empty
4	55	0.70	0.98	22	empty
5	436	0.66	0.78	56	empty

Interfaces

43 interfaces between chains.

N–Q · 1574 Å² buried · 5 hydrogen bonds · protein-protein
6–7 · 1554 Å² buried · 7 hydrogen bonds · protein-protein
2–3 · 1551 Å² buried · 9 hydrogen bonds · protein-protein
3–4 · 1550 Å² buried · 7 hydrogen bonds · protein-protein
5–6 · 1542 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6ZA9 · Fo domain of Ovine ATP synthase · the same entry in another collection · chain N against N, 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 P17605
Every structure of UniProt W5QEA9
Every structure of UniProt W5PP37
Every structure of UniProt O78752
Every structure of UniProt W5P5H1
Every structure of UniProt W5P913
Every structure of UniProt O78751
Every structure of UniProt W5QB48
Every structure of UniProt W5Q5U7
Every structure of UniProt W5PF18
Elsewhere: RCSB PDB 6ZA9 · PDBe 6ZA9 · UniProt P17605 · UniProt W5QEA9 · UniProt W5PP37 · UniProt O78752 · UniProt W5P5H1 · UniProt W5P913 · UniProt O78751 · UniProt W5QB48 · UniProt W5Q5U7 · UniProt W5PF18

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