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Crystal structure of nucleotide-free hexameric clpx

Analyse Crystal structure of nucleotide-free hexameric clpx in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3HTE
Type: protein
Length: 1,805 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-dependent clp protease ATP-binding subunit clpx
UniProt: P0A6H1
Ligands: SO4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 53% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP-dependent clp protease ATP-binding subunit clpx	protein	317	52% helix, 11% strand	P0A6H1
B	ATP-dependent clp protease ATP-binding subunit clpx	protein	309	53% helix, 11% strand	P0A6H1
C	ATP-dependent clp protease ATP-binding subunit clpx	protein	283	53% helix, 12% strand	P0A6H1
D	ATP-dependent clp protease ATP-binding subunit clpx	protein	301	52% helix, 12% strand	P0A6H1
E	ATP-dependent clp protease ATP-binding subunit clpx	protein	302	53% helix, 12% strand	P0A6H1
F	ATP-dependent clp protease ATP-binding subunit clpx	protein	293	55% helix, 12% strand	P0A6H1

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	788	0.82	0.85	89	SO4
2	807	0.82	0.84	86	SO4
3	896	0.79	0.81	88	SO4
4	1034	0.77	0.79	92	SO4
5	106	0.75	0.95	26	empty

Interfaces

6 interfaces between chains.

D–E · 1023 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 1005 Å² buried · 3 hydrogen bonds · protein-protein
A–F · 988 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 985 Å² buried · 3 hydrogen bonds · protein-protein
E–F · 947 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3HTE · Crystal structure of nucleotide-free hexameric ClpX · the same entry in another collection · chain F against F, TM-score 1.00
P0A6H1 · AlphaFold monomer V2.0 prediction for ATP-dependent clp protease ATP- binding subunit… · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P0A6H1
Elsewhere: RCSB PDB 3HTE · PDBe 3HTE · UniProt P0A6H1

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