Research workbench

Clpx-clpp complex bound to substrate and ATP-gamma-S, class 2

Analyse Clpx-clpp complex bound to substrate and ATP-gamma-S, class 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6POD
Type: protein
Length: 3,446 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-dependent clp protease ATP-binding subunit clpx; ATP-dependent clp protease…
EC: 3.4.21.92
UniProt: A0A1Q9L861, S1IIE7
Ligands: AGS, ADP
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 7 distinct chains · 45% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP-dependent clp protease ATP-binding subunit clpx	protein	329	45% helix, 11% strand	A0A1Q9L861
B	ATP-dependent clp protease ATP-binding subunit clpx	protein	350	46% helix, 12% strand	A0A1Q9L861
C, E	ATP-dependent clp protease ATP-binding subunit clpx	protein	351	45% helix, 11% strand	A0A1Q9L861
D	ATP-dependent clp protease ATP-binding subunit clpx	protein	352	44% helix, 11% strand	A0A1Q9L861
F	ATP-dependent clp protease ATP-binding subunit clpx	protein	350	44% helix, 11% strand	A0A1Q9L861
H, I, J, K, L, M, N	ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92)	protein	192	44% helix, 24% strand	S1IIE7
S	Substrate peptide	protein	19	21% helix, 0% strand	—

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 5 copies · chains B, C, D, E, F
ADP · Adenosine-5'-diphosphate · ligand · chains A, B

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

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	1111	0.86	0.87	132	empty
2	1130	0.86	0.87	113	AGS
3	764	0.81	0.85	66	AGS
4	761	0.81	0.84	62	AGS
5	627	0.80	0.85	66	AGS

Interfaces

38 interfaces between chains.

D–E · 2440 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 2384 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 2372 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 2312 Å² buried · 23 hydrogen bonds · protein-protein
H–I · 1781 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

6POD · ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 2 · the same entry in another collection · chain A against A, 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 A0A1Q9L861
Every structure of UniProt S1IIE7
Elsewhere: RCSB PDB 6POD · PDBe 6POD · UniProt A0A1Q9L861 · UniProt S1IIE7

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