4FOX

Crystal Structure of Mtb ThyA in complex with dUMP and Raltitrexed

PDB DOI: https://doi.org/10.2210/pdb4FOX/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-06-21 Released: 2013-08-07
Deposition Author(s): Reddy, M.C.M., Bruning, J.B., Sacchettini, J.C., Harshbarger, W., TB Structural Genomics Consortium (TBSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.258
R-Value Work: 0.213
R-Value Observed: 0.215

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of binary and ternary complexes of thymidylate synthase (ThyA) from Mycobacterium tuberculosis: Insights into the selectivity and mode of inhibition

Reddy, M.C.M., Bruning, J.B., Sacchettini, J.C., Harshbarger, W.

To be published.

Macromolecule Content

Total Structure Weight: 245.21 kDa
Atom Count: 17,259
Modelled Residue Count: 2,086
Deposited Residue Count: 2,104
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B, C, D, E A, B, C, D, E, F, G, H	263	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: MT2834, MTV002.29c, Rv2764c, thyA EC: 2.1.1.45
UniProt
Find proteins for P9WFR9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFR9 Go to UniProtKB: P9WFR9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WFR9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D16 Query on D16 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth C] SDF format, chain Q [auth E] SDF format, chain S [auth F] SDF format, chain U [auth G] SDF format, chain W [auth H] SDF format, chain L [auth B] SDF format, chain O [auth D] MOL2 format, chain I [auth A] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] MOL2 format, chain U [auth G] MOL2 format, chain W [auth H] MOL2 format, chain L [auth B] MOL2 format, chain O [auth D] mmCIF format, chain I [auth A] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F] mmCIF format, chain U [auth G] mmCIF format, chain W [auth H] mmCIF format, chain L [auth B] mmCIF format, chain O [auth D]	I [auth A] L [auth B] M [auth C] O [auth D] Q [auth E] I [auth A], L [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]	TOMUDEX C₂₁ H₂₂ N₄ O₆ S IVTVGDXNLFLDRM-HNNXBMFYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H]
UMP Query on UMP Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain T [auth F] SDF format, chain X [auth H] SDF format, chain V [auth G] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] MOL2 format, chain X [auth H] MOL2 format, chain V [auth G] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F] mmCIF format, chain X [auth H] mmCIF format, chain V [auth G]	J [auth A] K [auth B] N [auth C] P [auth D] R [auth E] J [auth A], K [auth B], N [auth C], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₈ P JSRLJPSBLDHEIO-SHYZEUOFSA-N		Interactions Focus chain J [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H] Interactions & Density Focus chain J [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.258
R-Value Work: 0.213
R-Value Observed: 0.215
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.342	α = 90
b = 138.444	β = 107
c = 99.948	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-08-07

Deposition Author(s):

TB Structural Genomics Consortium (TBSGC)

Revision History (Full details and data files)

Version 1.0: 2013-08-07
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description