1PZM

Crystal structure of HGPRT-ase from Leishmania tarentolae in complex with GMP

PDB DOI: https://doi.org/10.2210/pdb1PZM/pdb

Classification: TRANSFERASE
Organism(s): Leishmania tarentolae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2003-07-11 Released: 2004-07-27
Deposition Author(s): Monzani, P.S., Trapani, S., Oliva, G., Thiemann, O.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.215
R-Value Work: 0.173
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Leishmania tarentolae hypoxanthine-guanine phosphoribosyltransferase.

Monzani, P.S., Trapani, S., Thiemann, O.H., Oliva, G.

(2007) BMC Struct Biol 7: 59-59

PubMed: 17894860 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/1472-6807-7-59
Primary Citation of Related Structures:
1PZM

PubMed Abstract:
Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) (EC 2.4.2.8) is a central enzyme in the purine recycling pathway. Parasitic protozoa of the order Kinetoplastida cannot synthesize purines de novo and use the salvage pathway to synthesize purine bases, making this an attractive target for antiparasitic drug design.

Organizational Affiliation

Departamento de Física e Informática, Grupo de Cristalografia de Proteínas e Biologia Estrutural, Instituto de Física de São Carlos, USP, Caixa Postal 369, 13560-590, São Carlos - SP, Brazil. monzani@if.sc.usp.br

Macromolecule Content

Total Structure Weight: 48.05 kDa
Atom Count: 2,944
Modelled Residue Count: 340
Deposited Residue Count: 422
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypoxanthine-guanine phosphoribosyltransferase	A, B	211	Leishmania tarentolae	Mutation(s): 0 Gene Names: hgprt EC: 2.4.2.8
UniProt
Find proteins for Q9NJI5 (Leishmania tarentolae) Explore Q9NJI5 Go to UniProtKB: Q9NJI5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NJI5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5GP Query on 5GP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	GUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P RQFCJASXJCIDSX-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.215
R-Value Work: 0.173
R-Value Observed: 0.175
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.104	α = 90
b = 85.443	β = 90
c = 87.598	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-07-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-07-27
Type: Initial release
Version 1.1: 2007-11-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2023-08-16
Changes: Data collection, Database references, Derived calculations, Refinement description