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Cryo-EM structure of tetrahymena thermophila mitochondrial ATP synthase - central STALK/CRING

Analyse Cryo-EM structure of tetrahymena thermophila mitochondrial ATP synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YNW
Type: protein
Length: 1,176 residues
Chains: 13
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Subunit C; Subunit gamma; Subunit delta; Subunit epsilon
EC: 3.6.1.34
UniProt: Q951A5, Q22Z05, Q22ZH1, I7MMW3
Pockets: 8 · best druggability 0.79

Structure

electron microscopy · 4 distinct chains · 47% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P, O, N, M, L, K, J, I, H, Q	Subunit C (EC 3.6.1.34)	protein	75	95% helix, 0% strand	Q951A5
g	Subunit gamma	protein	224	54% helix, 15% strand	Q22Z05
d	Subunit delta	protein	134	18% helix, 40% strand	Q22ZH1
e	Subunit epsilon	protein	68	31% helix, 15% strand	I7MMW3

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	969	0.79	0.81	105	empty
2	533	0.77	0.84	57	empty
3	681	0.64	0.74	73	empty
4	226	0.60	0.81	27	empty
5	268	0.56	0.75	29	empty

Interfaces

32 interfaces between chains.

H–Q · 1613 Å² buried · 1 hydrogen bond · protein-protein
J–I · 1603 Å² buried · 3 hydrogen bonds · protein-protein
N–M · 1601 Å² buried · 1 hydrogen bond · protein-protein
I–H · 1600 Å² buried · 4 hydrogen bonds · protein-protein
L–K · 1573 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6YNW · Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase - central… · the same entry in another collection · chain P against P, 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 Q951A5
Every structure of UniProt Q22Z05
Every structure of UniProt Q22ZH1
Every structure of UniProt I7MMW3
Elsewhere: RCSB PDB 6YNW · PDBe 6YNW · UniProt Q951A5 · UniProt Q22Z05 · UniProt Q22ZH1 · UniProt I7MMW3

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