MolNFT v1 · #171848 · protein

Bovine ATP synthase rotor domain, state 3

6ZIK · ATP synthase subunit gamma, mitochondrial: “Bovine ATP synthase rotor domain, state 3”. Electron microscopy, 8 pockets (best druggability 0.84). MolNFT v1 #171848 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ZIK
Type: protein
Length: 1,048 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase subunit gamma, mitochondrial; ATP synthase subunit delta, mitochondrial; ATP…
UniProt: P05631, P05630, P05632, P07926
Pockets: 8 · best druggability 0.84

Structure

electron microscopy · 5 distinct chains · 62% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	ATP synthase subunit gamma, mitochondrial	protein	272	64% helix, 14% strand	P05631
H	ATP synthase subunit delta, mitochondrial	protein	132	26% helix, 39% strand	P05630
I	ATP synthase subunit epsilon, mitochondrial	protein	47	55% helix, 9% strand	P05632
K, L, P	ATP synthase F(0) complex subunit C2, mitochondrial	protein	74	91% helix, 0% strand	P07926
M, N, Q, R, O	ATP synthase F(0) complex subunit C2, mitochondrial	protein	75	95% helix, 0% strand	P07926

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	449	0.84	0.91	50	empty
2	324	0.81	0.91	36	empty
3	103	0.69	0.92	26	empty
4	90	0.67	0.92	22	empty
5	208	0.57	0.80	35	empty

Interfaces

29 interfaces between chains.

P–Q · 1648 Å² buried · 9 hydrogen bonds · protein-protein
Q–R · 1565 Å² buried · 6 hydrogen bonds · protein-protein
P–O · 1529 Å² buried · 4 hydrogen bonds · protein-protein
L–M · 1516 Å² buried · 1 hydrogen bond · protein-protein
N–O · 1499 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (methylation).

Compared structures

6ZIK · bovine ATP synthase rotor domain, state 3 · the same entry in another collection · chain O against O, TM-score 1.00
P07926 · AlphaFold monomer V2.0 prediction for ATP synthase F(0) complex subunit C2, mitochondrial… · a predicted model of the same protein · chain Q 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 P05631
Every structure of UniProt P05630
Every structure of UniProt P05632
Every structure of UniProt P07926
Elsewhere: RCSB PDB 6ZIK · PDBe 6ZIK · UniProt P05631 · UniProt P05630 · UniProt P05632 · UniProt P07926

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