5T7O

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
R-Value Work: 0.177
R-Value Observed: 0.179

Starting Model: experimental
View more details

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
Modelled Residue Count: 1,965
Deposited Residue Count: 2,084
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 AB [auth D] SDF format, chain F [auth A] SDF format, chain KA [auth C] SDF format, chain V [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain F [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain V [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain F [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain V [auth B]	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 G [auth A] SDF format, chain MA [auth C] SDF format, chain W [auth B] SDF format, chain ZA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain ZA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain ZA [auth D]	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 AA [auth B] SDF format, chain BA [auth B] SDF format, chain BB [auth D] SDF format, chain CA [auth B] SDF format, chain CB [auth D] SDF format, chain DA [auth B] SDF format, chain DB [auth D] SDF format, chain EA [auth B] SDF format, chain EB [auth D] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain GB [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain HB [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain JB [auth D] SDF format, chain K [auth A] SDF format, chain KB [auth D] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain S [auth A] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain U [auth A] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain FB [auth D] SDF format, chain IB [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain PA [auth C] SDF format, chain T [auth A] SDF format, chain UA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain JB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain IB [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain PA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain UA [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain JB [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KB [auth D] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain FB [auth D] mmCIF format, chain IB [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain PA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain UA [auth C]	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
R-Value Work: 0.177
R-Value Observed: 0.179
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

View Full Validation Report

Ligand Structure Quality Assessment

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