5T7O | pdb_00005t7o

Crystal structure of Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase in complex with (6S)-5,6,7,8-TETRAHYDROFOLATE

PDB DOI: https://doi.org/10.2210/pdb5T7O/pdb

Classification: OXIDOREDUCTASE
Organism(s): Trypanosoma cruzi strain CL Brener
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-09-05 Released: 2017-09-20
Deposition Author(s): Di Pisa, F., Dello Iacono, L., Bonucci, A., Mangani, S.
Funding Organization(s): European Union

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.220 (Depositor), 0.254 (DCC)
R-Value Work:
0.177 (Depositor)
R-Value Observed:
0.179 (Depositor)

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

Crystal structure of Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase in complex with (6S)-5,6,7,8-TETRAHYDROFOLATE

Di Pisa, F., Dello Iacono, L., Bonucci, A., Mangani, S.

To be published.

Macromolecule Content

Total Structure Weight: 244.62 kDa
Atom Count: 18,488
Modeled Residue Count: 1,965
Deposited Residue Count: 2,084
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional dihydrofolate reductase-thymidylate synthase	A, B, C, D	521	Trypanosoma cruzi strain CL Brener	Mutation(s): 0 Gene Names: Tc00.1047053509153.90
UniProt
Find proteins for Q4DLS1 (Trypanosoma cruzi (strain CL Brener)) Explore Q4DLS1 Go to UniProtKB: Q4DLS1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4DLS1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain LA [auth C] SDF format, chain X [auth B] SDF format, chain YA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain YA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain YA [auth D]	E [auth A], LA [auth C], X [auth B], YA [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain LA [auth C] Focus chain X [auth B] Focus chain YA [auth D] Interactions & Density Focus chain E [auth A] Focus chain LA [auth C] Focus chain X [auth B] Focus chain YA [auth D]
THG Query on THG Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain KA [auth C] SDF format, chain F [auth A] SDF format, chain AB [auth D] MOL2 format, chain V [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain AB [auth D] mmCIF format, chain V [auth B] mmCIF format, chain KA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain AB [auth D]	AB [auth D], F [auth A], KA [auth C], V [auth B]	(6S)-5,6,7,8-TETRAHYDROFOLATE C₁₉ H₂₃ N₇ O₆ MSTNYGQPCMXVAQ-RYUDHWBXSA-N		Interactions Focus chain AB [auth D] Focus chain F [auth A] Focus chain KA [auth C] Focus chain V [auth B] Interactions & Density Focus chain AB [auth D] Focus chain F [auth A] Focus chain KA [auth C] Focus chain V [auth B]
UMP Query on UMP Download:Ideal Coordinates CCD File SDF format, chain ZA [auth D] SDF format, chain W [auth B] SDF format, chain MA [auth C] SDF format, chain G [auth A] MOL2 format, chain ZA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain G [auth A] mmCIF format, chain ZA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain MA [auth C] mmCIF format, chain G [auth A]	G [auth A], MA [auth C], W [auth B], ZA [auth D]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₈ P JSRLJPSBLDHEIO-SHYZEUOFSA-N		Interactions Focus chain G [auth A] Focus chain MA [auth C] Focus chain W [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain G [auth A] Focus chain MA [auth C] Focus chain W [auth B] Focus chain ZA [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain XA [auth C] SDF format, chain WA [auth C] SDF format, chain VA [auth C] SDF format, chain UA [auth C] SDF format, chain U [auth A] SDF format, chain TA [auth C] SDF format, chain T [auth A] SDF format, chain SA [auth C] SDF format, chain S [auth A] SDF format, chain RA [auth C] SDF format, chain R [auth A] SDF format, chain QA [auth C] SDF format, chain Q [auth A] SDF format, chain PA [auth C] SDF format, chain P [auth A] SDF format, chain OA [auth C] SDF format, chain O [auth A] SDF format, chain NA [auth C] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain KB [auth D] SDF format, chain K [auth A] SDF format, chain JB [auth D] SDF format, chain JA [auth B] SDF format, chain J [auth A] SDF format, chain IB [auth D] SDF format, chain IA [auth B] SDF format, chain I [auth A] SDF format, chain HB [auth D] SDF format, chain HA [auth B] SDF format, chain H [auth A] SDF format, chain GB [auth D] SDF format, chain GA [auth B] SDF format, chain FB [auth D] SDF format, chain FA [auth B] SDF format, chain EB [auth D] SDF format, chain EA [auth B] SDF format, chain DB [auth D] SDF format, chain DA [auth B] SDF format, chain CB [auth D] SDF format, chain CA [auth B] SDF format, chain BB [auth D] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain KB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain JB [auth D] MOL2 format, chain JA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain IB [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain HB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain XA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain KB [auth D] mmCIF format, chain K [auth A] mmCIF format, chain JB [auth D] mmCIF format, chain JA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain IB [auth D] mmCIF format, chain IA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain HB [auth D] mmCIF format, chain HA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain GB [auth D] mmCIF format, chain GA [auth B] mmCIF format, chain FB [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain EB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain BB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] BB [auth D] CA [auth B] CB [auth D] AA [auth B], BA [auth B], BB [auth D], CA [auth B], CB [auth D], DA [auth B], DB [auth D], EA [auth B], EB [auth D], FA [auth B], FB [auth D], GA [auth B], GB [auth D], H [auth A], HA [auth B], HB [auth D], I [auth A], IA [auth B], IB [auth D], J [auth A], JA [auth B], JB [auth D], K [auth A], KB [auth D], L [auth A], M [auth A], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], VA [auth C], WA [auth C], XA [auth C], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KB [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KB [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.220 (Depositor), 0.254 (DCC)
R-Value Work: 0.177 (Depositor)
R-Value Observed: 0.179 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.547	α = 90
b = 173.54	β = 90
c = 174.159	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-09-20

Deposition Author(s):

Funding Organization	Location	Grant Number
European Union	Italy	603240

Revision History (Full details and data files)

Version 1.0: 2017-09-20
Type: Initial release
Version 1.1: 2019-10-16
Changes: Data collection
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description