Research workbench

Porcine ATP synthase fo domain

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

PDB: 6ZMR
Type: protein
Length: 1,279 residues
Chains: 17
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase protein 8; ATP synthase F(0) complex subunit C1, mitochondrial; ATP synthase…
UniProt: Q35914, F1RWF6, Q35915, A0A286ZYM6, A0A287A2Y4, Q9MYT8, Q95339, F1SAK7, A0A4X1TX70, F1RFD4
Ligands: CDL
Pockets: 19 · best druggability 0.87

Structure

electron microscopy · 11 distinct chains · 75% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
8	ATP synthase protein 8	protein	34	82% helix, 0% strand	Q35914
K, L, P	ATP synthase F(0) complex subunit C1, mitochondrial	protein	74	92% helix, 0% strand	F1RWF6
M, N, O, Q, R	ATP synthase F(0) complex subunit C1, mitochondrial	protein	75	92% helix, 0% strand	F1RWF6
a	ATP synthase subunit a	protein	223	72% helix, 0% strand	Q35915
b	ATP synthase peripheral stalk-membrane subunit B	protein	94	66% helix, 4% strand	A0A286ZYM6
d	ATP synthase subunit D, mitochondrial	protein	34	38% helix, 0% strand	A0A287A2Y4
e	ATP synthase subunit E, mitochondrial	protein	57	86% helix, 0% strand	Q9MYT8
f	ATP synthase subunit F, mitochondrial	protein	83	58% helix, 1% strand	Q95339
g	ATP synthase G subunit	protein	74	78% helix, 1% strand	F1SAK7
j	ATP synthase J subunit (6.8PL)	protein	48	85% helix, 0% strand	A0A4X1TX70
k	ATP synthase membrane subunit dapit	protein	35	77% helix, 0% strand	F1RFD4

Ligands and binding sites

CDL · Cardiolipin · ligand · chains a, b, f

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

Pockets

19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	896	0.87	0.88	94	empty
2	498	0.79	0.86	51	empty
3	604	0.76	0.82	72	CDL
4	458	0.69	0.79	44	empty
5	331	0.64	0.79	35	empty

Interfaces

32 interfaces between chains.

P–Q · 1639 Å² buried · 12 hydrogen bonds · protein-protein
Q–R · 1613 Å² buried · 8 hydrogen bonds · protein-protein
L–M · 1526 Å² buried · 5 hydrogen bonds · protein-protein
8–a · 1520 Å² buried · 8 hydrogen bonds · protein-protein
O–P · 1516 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (methylation).

Compared structures

6ZMR · Porcine ATP synthase Fo domain · the same entry in another collection · chain k against k, 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 Q35914
Every structure of UniProt F1RWF6
Every structure of UniProt Q35915
Every structure of UniProt A0A286ZYM6
Every structure of UniProt A0A287A2Y4
Every structure of UniProt Q9MYT8
Every structure of UniProt Q95339
Every structure of UniProt F1SAK7
Every structure of UniProt A0A4X1TX70
Every structure of UniProt F1RFD4
Elsewhere: RCSB PDB 6ZMR · PDBe 6ZMR · UniProt Q35914 · UniProt F1RWF6 · UniProt Q35915 · UniProt A0A286ZYM6 · UniProt A0A287A2Y4 · UniProt Q9MYT8 · UniProt Q95339 · UniProt F1SAK7 · UniProt A0A4X1TX70 · UniProt F1RFD4

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