MolNFT v1 · #47844 · protein

Crystal structure of the 5'-deoxynucleotidase yfbr

2PAQ: “Crystal structure of the 5'-deoxynucleotidase yfbr”. X-ray diffraction, 4 pockets (best druggability 0.65). MolNFT v1 #47844 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2PAQ
Type: protein
Length: 353 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-deoxynucleotidase yfbr
EC: 3.1.3.5
UniProt: P76491
Pockets: 4 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 69% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-deoxynucleotidase yfbr (EC 3.1.3.5)	protein	177	68% helix, 1% strand	P76491
B	5'-deoxynucleotidase yfbr (EC 3.1.3.5)	protein	176	70% helix, 1% strand	P76491

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	349	0.65	0.80	35	empty
2	355	0.62	0.78	29	empty
3	105	0.41	0.77	20	empty
4	83	0.37	0.76	20	empty

Interfaces

1 interface between chains.

A–B · 2376 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

2PAQ · Crystal structure of the 5'-deoxynucleotidase YfbR · the same entry in another collection · chain A against A, TM-score 1.00
P76491 · AlphaFold monomer V2.0 prediction for 5'-deoxynucleotidase yfbr (P76491) · a predicted model of the same protein · chain B 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 P76491
Elsewhere: RCSB PDB 2PAQ · PDBe 2PAQ · UniProt P76491

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