MolNFT v1 · #28773 · protein

Crystal structure of a the E. COLI pyrimidine nucleoside hydrolase ybek with bound ribose

1YOE · Hypothetical protein ybek: “Crystal structure of a the E. COLI pyrimidine nucleoside hydrolase ybek with bound ribose”. X-ray diffraction, 2 ligands (RIB, CA), 1 pocket (best druggability 0.63). MolNFT v1 #28773 on GenesisL1: 3D…

PDB: 1YOE
Type: protein
Length: 302 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein ybek
EC: 3.2.2.8
UniProt: P41409
Ligands: RIB, CA
Pockets: 1 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical protein ybek (EC 3.2.2.8)	protein	302	39% helix, 19% strand	P41409

Ligands and binding sites

RIB · alpha-D-ribofuranose · ligand · chains A
CA · Calcium ion · metal · 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	279	0.63	0.80	37	RIB

Compared structures

1YOE · Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose · the same entry in another collection · chain A against A, TM-score 1.00
P41409 · AlphaFold monomer V2.0 prediction for pyrimidine-specific ribonucleoside hydrolase riha… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P41409
Elsewhere: RCSB PDB 1YOE · PDBe 1YOE · UniProt P41409

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