MolNFT v1 · #171772 · protein

Bovine ATP synthase rotor domain state 2

6ZG8 · ATP synthase subunit gamma, mitochondrial: “Bovine ATP synthase rotor domain state 2”. Electron microscopy, 6 pockets (best druggability 0.89). MolNFT v1 #171772 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ZG8
Type: protein
Length: 1,045 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: 6 · best druggability 0.89

Structure

electron microscopy · 5 distinct chains · 61% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	ATP synthase subunit gamma, mitochondrial	protein	272	62% helix, 14% strand	P05631
H	ATP synthase subunit delta, mitochondrial	protein	133	29% helix, 40% strand	P05630
I	ATP synthase subunit epsilon, mitochondrial	protein	47	55% helix, 6% strand	P05632
K, M, N, O, P, Q, R	ATP synthase F(0) complex subunit C2, mitochondrial	protein	74	89% helix, 0% strand	P07926
L	ATP synthase F(0) complex subunit C2, mitochondrial	protein	75	91% helix, 0% strand	P07926

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	887	0.89	0.91	99	empty
2	672	0.73	0.80	55	empty
3	247	0.59	0.79	43	empty
4	95	0.57	0.86	24	empty
5	65	0.48	0.84	14	empty

Interfaces

27 interfaces between chains.

K–L · 1622 Å² buried · 8 hydrogen bonds · protein-protein
O–P · 1564 Å² buried · 5 hydrogen bonds · protein-protein
Q–R · 1519 Å² buried · 7 hydrogen bonds · protein-protein
N–O · 1519 Å² buried · 6 hydrogen bonds · protein-protein
K–R · 1506 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (methylation).

Compared structures

6ZG8 · bovine ATP synthase rotor domain state 2 · the same entry in another collection · chain R against R, TM-score 1.00
P05630 · AlphaFold monomer V2.0 prediction for ATP synthase subunit delta, mitochondrial (P05630) · a predicted model of the same protein · chain H 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 6ZG8 · PDBe 6ZG8 · UniProt P05631 · UniProt P05630 · UniProt P05632 · UniProt P07926

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