3IOM

Crystal structure of Purine Nucleoside Phosphorylase from Mycobacterium tuberculosis in complex with 2'-Deoxyguanosine

PDB DOI: https://doi.org/10.2210/pdb3IOM/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-08-14 Released: 2011-01-12
Deposition Author(s): de Azevedo Jr., W.F., Basso, L.A., Santos, D.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.249
R-Value Work: 0.175
R-Value Observed: 0.179

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystallographic and docking studies of purine nucleoside phosphorylase from Mycobacterium tuberculosis.

Ducati, R.G., Basso, L.A., Santos, D.S., de Azevedo, W.F.

(2010) Bioorg Med Chem 18: 4769-4774

PubMed: 20570524 Search on PubMed
DOI: https://doi.org/10.1016/j.bmc.2010.05.009
Primary Citation of Related Structures:
3IOM

PubMed Abstract:
This work describes for the first time the structure of purine nucleoside phosphorylase from Mycobacterium tuberculosis (MtPNP) in complex with sulfate and its natural substrate, 2'-deoxyguanosine, and its application to virtual screening. We report docking studies of a set of molecules against this structure. Application of polynomial empirical scoring function was able to rank docking solutions with good predicting power which opens the possibility to apply this new criterion to analyze docking solutions and screen small-molecule databases for new chemical entities to inhibit MtPNP.

Organizational Affiliation

Centro de Pesquisas em Biologia Molecular e Funcional, Instituto de Pesquisas Biomédicas, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Avenida Ipiranga 6681/92-A, 90619-900 Porto Alegre, RS, Brazil.

Macromolecule Content

Total Structure Weight: 55.93 kDa
Atom Count: 4,049
Modelled Residue Count: 524
Deposited Residue Count: 536
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase	A, B	268	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: deoD, MT3406, MTV016.06, punA, punA (deoD) (Rv3307) (MT3406) (MTV016.06), Rv3307 EC: 2.4.2.1
UniProt
Find proteins for P9WP01 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WP01 Go to UniProtKB: P9WP01
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WP01
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNG Query on GNG Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	2'-DEOXY-GUANOSINE C₁₀ H₁₃ N₅ O₄ YKBGVTZYEHREMT-KVQBGUIXSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.249
R-Value Work: 0.175
R-Value Observed: 0.179
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.48	α = 90
b = 113.48	β = 90
c = 85.011	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-01-12

Deposition Author(s):

de Azevedo Jr., W.F.

Basso, L.A.

Santos, D.S.

Revision History (Full details and data files)

Version 1.0: 2011-01-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description