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Crystal structure of E.coli RppH in complex with ppcpA

Analyse Crystal structure of E.coli RppH in complex with ppcpA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VCO
Type: protein
Length: 159 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.7
Source: Escherichia coli (strain K12)
Molecule: RNA pyrophosphohydrolase
EC: 3.6.1.-
UniProt: P0A776
Ligands: APC
Pockets: 2 · best druggability 0.29

Structure

x-ray diffraction · resolution 1.7 · 1 distinct chain · 30% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA pyrophosphohydrolase (EC 3.6.1.-)	protein	159	30% helix, 32% strand	P0A776

Ligands and binding sites

APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	76	0.29	0.73	19	empty
2	56	0.28	0.74	18	APC

Compared structures

6VCO · Crystal structure of E.COLI rpph in complex with ppcpa · the same entry in another collection · chain A against A, TM-score 1.00
P0A776 · AlphaFold monomer V2.0 prediction for RNA pyrophosphohydrolase (P0A776) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P0A776
Elsewhere: RCSB PDB 6VCO · PDBe 6VCO · UniProt P0A776

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