5CHP | pdb_00005chp

T. maritima ThyX in complex with TyC5-03

PDB DOI: https://doi.org/10.2210/pdb5CHP/pdb

Classification: HYDROLASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-07-10 Released: 2016-10-19
Deposition Author(s): Surade, S., Luciani, R., Saxena, P., Santucci, M., Ferrari, S., Venturelli, A., Marverti, G., Ponterini, G., Abell, C.A., Blundell, T.L., Costi, M.P.
Funding Organization(s): EU FP6

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.201 (Depositor), 0.204 (DCC)
R-Value Work:
0.170 (Depositor)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Identification of inhibitors targeting substrate-binding site in Mycobacterium tuberculosis FAD-dependent Thymidylate synthase (ThyX) through Virtual Screening: A New study de-fining the binding mechanism of Inhibitors

Surade, S.

To be published.

Macromolecule Content

Total Structure Weight: 28.78 kDa
Atom Count: 2,109
Modeled Residue Count: 217
Deposited Residue Count: 234
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase ThyX	A	234	Thermotoga maritima	Mutation(s): 0 Gene Names: thyX, thy1, TM_0449 EC: 2.1.1.148
UniProt
Find proteins for Q9WYT0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYT0 Go to UniProtKB: Q9WYT0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WYT0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
51Q Query on 51Q Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(2S)-2-[(3-hydroxy-5-oxo-4,5-dihydro-1,2,4-triazin-6-yl)sulfanyl]propanoic acid C₆ H₇ N₃ O₄ S RHHZZMNGKMZLIA-REOHCLBHSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.201 (Depositor), 0.204 (DCC)
R-Value Work: 0.170 (Depositor)
R-Value Observed: 0.171 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.58	α = 90
b = 110.58	β = 90
c = 122.96	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-10-19

Deposition Author(s):

Funding Organization	Location	Grant Number
EU FP6	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2016-10-19
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.