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Structure of the E. COLI inosine triphosphate pyrophosphatase rgdb in complex with imp

Analyse Structure of the E. COLI inosine triphosphate pyrophosphatase rgdb in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2PYU
Type: protein
Length: 208 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inosine triphosphate pyrophosphatase rdgb
EC: 3.6.1.19
UniProt: P52061
Ligands: IMP
Pockets: 1 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Inosine triphosphate pyrophosphatase rdgb (EC 3.6.1.19)	protein	208	39% helix, 23% strand	P52061

Ligands and binding sites

IMP · Inosinic acid · ligand · chains A
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	319	0.59	0.77	39	IMP

Compared structures

2PYU · Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with IMP · the same entry in another collection · chain A against A, TM-score 1.00
P52061 · AlphaFold monomer V2.0 prediction for DITP/XTP pyrophosphatase (P52061) · a predicted model of the same protein · chain A against A, TM-score 0.87

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 P52061
Elsewhere: RCSB PDB 2PYU · PDBe 2PYU · UniProt P52061

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