PDBsum entry 3d1v

Transferase

PDB id: 3d1v

Contents

Protein chain

288 a.a. *

Ligands

SO4 ×3

D1V

Waters ×69

* Residue conservation analysis

PDB id:

3d1v

Name:

Transferase

Title:

Crystal structure of human pnp complexed with 2-mercapto(3h) quinazolinone

Structure:

Purine nucleoside phosphorylase. Chain: a. Synonym: inosine phosphorylase, pnp. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: np, pnp. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.70Å R-factor: 0.224 R-free: 0.277

Authors:

W.F.De Azevedo Jr.,L.A.Basso,D.S.Santos

Key ref:

L.F.Timmers et al. (2008). Structural studies of human purine nucleoside phosphorylase: towards a new specific empirical scoring function. Arch Biochem Biophys, 479, 28-38. PubMed id: 18790691

Date:

06-May-08 Release date: 14-Jul-09

Protein chain

P00491  (PNPH_HUMAN) -  Purine nucleoside phosphorylase from Homo sapiens

Seq: 289 a.a.

Struc: 288 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.4.2.1 - purine-nucleoside phosphorylase.
• Reaction:
  1. a purine D-ribonucleoside + phosphate = a purine nucleobase + alpha- D-ribose 1-phosphate
  2. a purine 2'-deoxy-D-ribonucleoside + phosphate = a purine nucleobase + 2-deoxy-alpha-D-ribose 1-phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Arch Biochem Biophys 479:28-38 (2008)

PubMed id: 18790691

Structural studies of human purine nucleoside phosphorylase: towards a new specific empirical scoring function.

L.F.Timmers, R.A.Caceres, A.L.Vivan, L.M.Gava, R.Dias, R.G.Ducati, L.A.Basso, D.S.Santos, W.F.de Azevedo.

ABSTRACT

Human purine nucleoside phosphorylase (HsPNP) is a target for inhibitor development aiming at T-cell immune response modulation. In this work, we report the development of a new set of empirical scoring functions and its application to evaluate binding affinities and docking results. To test these new functions, we solved the structure of HsPNP and 2-mercapto-4(3H)-quinazolinone (HsPNP:MQU) binary complex at 2.7A resolution using synchrotron radiation, and used these functions to predict ligand position obtained in docking simulations. We also employed molecular dynamics simulations to analyze HsPNP in two conditions, as apoenzyme and in the binary complex form, in order to assess the structural features responsible for stability. Analysis of the structural differences between systems provides explanation for inhibitor binding. The use of these scoring functions to evaluate binding affinities and molecular docking results may be used to guide future efforts on virtual screening focused on HsPNP.