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Cryo-EM structure of the clpx component of the CLPXP1/2 degradation machinery.

Analyse Cryo-EM structure of the clpx component of the CLPXP1/2 degradation machinery. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6SFW
Type: protein
Length: 1,955 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-dependent clp protease ATP-binding subunit clpx
UniProt: L8DZH5
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 6 distinct chains · 50% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
O	ATP-dependent clp protease ATP-binding subunit clpx	protein	320	53% helix, 10% strand	L8DZH5
P	ATP-dependent clp protease ATP-binding subunit clpx	protein	327	51% helix, 11% strand	L8DZH5
Q	ATP-dependent clp protease ATP-binding subunit clpx	protein	316	51% helix, 11% strand	L8DZH5
R	ATP-dependent clp protease ATP-binding subunit clpx	protein	326	48% helix, 11% strand	L8DZH5
S	ATP-dependent clp protease ATP-binding subunit clpx	protein	332	47% helix, 10% strand	L8DZH5
T	ATP-dependent clp protease ATP-binding subunit clpx	protein	334	48% helix, 11% strand	L8DZH5

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	938	0.89	0.90	135	empty
2	746	0.82	0.85	82	empty
3	1060	0.81	0.82	100	empty
4	1198	0.80	0.82	104	empty
5	318	0.79	0.90	54	empty

Interfaces

6 interfaces between chains.

S–T · 2006 Å² buried · 28 hydrogen bonds · protein-protein
Q–R · 1977 Å² buried · 19 hydrogen bonds · protein-protein
R–S · 1792 Å² buried · 19 hydrogen bonds · protein-protein
P–Q · 1693 Å² buried · 24 hydrogen bonds · protein-protein
O–T · 1604 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

6SFW · Cryo-EM Structure of the ClpX component of the ClpXP1/2 degradation machinery. · the same entry in another collection · chain O against O, 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 L8DZH5
Elsewhere: RCSB PDB 6SFW · PDBe 6SFW · UniProt L8DZH5

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