1P33 | pdb_00001p33

Pteridine reductase from Leishmania tarentolae complex with NADPH and MTX

PDB DOI: https://doi.org/10.2210/pdb1P33/pdb

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

Deposited: 2003-04-16 Released: 2003-09-02
Deposition Author(s): Zhao, H., Bray, T., Ouellette, M., Zhao, M., Ferre, R.A., Matthews, D., Whiteley, J.M., Varughese, K.I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.86 Å
R-Value Free:
0.251 (Depositor), 0.243 (DCC)
R-Value Work:
0.213 (Depositor), 0.208 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of pteridine reductase (PTR1) from Leishmania tarentolae.

Zhao, H., Bray, T., Ouellette, M., Zhao, M., Ferre, R.A., Matthews, D., Whiteley, J.M., Varughese, K.I.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1539-1544

PubMed: 12925782 Search on PubMed
DOI: https://doi.org/10.1107/s0907444903013131
Primary Citation Related Structures:
1P33

PubMed Abstract:
The protozoan parasites Leishmania utilize a pteridine-reducing enzyme, pteridine reductase (PTR1), to bypass antifolate inhibition. The crystal structure of PTR1 from L. tarentolae has been solved as a binary complex with NADPH at 2.8 A resolution. The structure was solved by molecular-replacement techniques using the recently reported L. major PTR1 structure as a search model. Comparisons of the present structure with the L. major PTR1 allowed us to identify regions of flexibility in the molecule. PTR1 is a member of the growing family of short-chain dehydrogenases (SDR) which share the characteristic Tyr(Xaa)(3)Lys motif in the vicinity of the active site. The functional enzyme is a tetramer and the crystallographic asymmetric unit contains a tetramer with 222 point-group symmetry.

Organizational Affiliation

Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 127.89 kDa
Atom Count: 8,564
Modeled Residue Count: 1,072
Deposited Residue Count: 1,156
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pteridine reductase 1	A, B, C, D	289	Leishmania tarentolae	Mutation(s): 0 Gene Names: PTR1 OR LTDH EC: 1.1.1.253 (PDB Primary Data), 1.5.1.33 (UniProt)
UniProt
Find proteins for P42556 (Leishmania tarentolae) Explore P42556 Go to UniProtKB: P42556
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42556
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
MTX Query on MTX Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	METHOTREXATE C₂₀ H₂₂ N₈ O₅ FBOZXECLQNJBKD-ZDUSSCGKSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.86 Å
R-Value Free: 0.251 (Depositor), 0.243 (DCC)
R-Value Work: 0.213 (Depositor), 0.208 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.301	α = 90
b = 96.103	β = 90
c = 195.545	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2003-09-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-09-02
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-16
Changes: Data collection, Database references, Derived calculations, Refinement description