MolNFT v2 · #34838 · protein

Structure of the ZBD-XB complex

2DS8 · ATP-dependent Clp protease ATP-binding subunit clpX: “Structure of the ZBD-XB complex”. X-ray diffraction at 1.6, 1 ligand (ZN). MolNFT v2 #34838 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2DS8
Type: protein
Length: 96 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.6
Source: Escherichia coli; SYNTHETIC CONSTRUCT
Molecule: ATP-dependent Clp protease ATP-binding subunit clpX; SspB-tail peptide
UniProt: P0A6H1
Ligands: ZN

Structure

x-ray diffraction · resolution 1.6 · 3 distinct chains · 31% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP-dependent Clp protease ATP-binding subunit clpX	protein	43	28% helix, 19% strand	P0A6H1
P, Q	SspB-tail peptide	protein	6	0% helix, 33% strand	—
B	ATP-dependent Clp protease ATP-binding subunit clpX	protein	41	39% helix, 24% strand	P0A6H1

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

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

Interfaces

5 interfaces between chains.

A–B · 718 Å² buried · 3 hydrogen bonds · protein-protein
P–B · 384 Å² buried · 10 hydrogen bonds · protein-protein
A–Q · 356 Å² buried · 7 hydrogen bonds · protein-protein
B–Q · 159 Å² buried · 0 hydrogen bonds · protein-protein
A–P · 145 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2DS8 · Structure of the zbd-xb complex · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.92

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 2DS8 · PDBe 2DS8 · UniProt P0A6H1

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