Macromolecule Content

Total Structure Weight: 62.61 kDa
Atom Count: 4,600
Modelled Residue Count: 530
Deposited Residue Count: 530
Unique protein chains: 1

1AXW

E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH METHOTREXATE (MTX) AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)

PDB DOI: https://doi.org/10.2210/pdb1AXW/pdb

Classification: METHYLTRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1997-10-23 Released: 1998-10-28
Deposition Author(s): Stout, T.J., Sage, C.R., Stroud, R.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.265
R-Value Work: 0.217
R-Value Observed: 0.217

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Discovery of Thymidylate Synthase Inhibitors Using Flexible Docking and an Empirically Tuned Scoring Function

Welch, W., Sage, C.R., Stout, T.J., Klein, T., Ruppert, J., Stroud, R.M., Jain, A.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDYLATE SYNTHASE	A, B	265	Escherichia coli	Mutation(s): 0 Gene Names: thyA EC: 2.1.1.45
UniProt
Find proteins for P0A884 (Escherichia coli (strain K12)) Explore P0A884 Go to UniProtKB: P0A884
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A884
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MTX Query on MTX Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	METHOTREXATE C₂₀ H₂₂ N₈ O₅ FBOZXECLQNJBKD-ZDUSSCGKSA-N		Ligand Interaction
UMP Query on UMP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₈ P JSRLJPSBLDHEIO-SHYZEUOFSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.265
R-Value Work: 0.217
R-Value Observed: 0.217
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.34	α = 90
b = 127.34	β = 90
c = 68.06	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1998-10-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1998-10-28
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.