4PSG | pdb_00004psg

Crystal Structure of C.elegans Thymidylate Synthase in complex with an inhibitor N(4)OHdCMP

• PDB DOI: https://doi.org/10.2210/pdb4PSG/pdb

• Classification: TRANSFERASE/transferase inhibitor
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-03-07 Released: 2015-02-18 
• Deposition Author(s): Wilk, P., Jarmula, A., Rode, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.267 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

Crystal Structure of C.elegans Thymidylate Synthase in complex with an inhibitor N(4)OHdCMP

Dowiercia, A., Wilk, P., Rypniewski, W., Rode, W., Jarmua, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72.36 kDa 
• Atom Count: 4,755 
• Modeled Residue Count: 578 
• Deposited Residue Count: 630 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B	315	Caenorhabditis elegans	Mutation(s): 0  EC: 2.1.1.45
UniProt
Find proteins for Q9Y052 (Caenorhabditis elegans) Explore Q9Y052  Go to UniProtKB:  Q9Y052

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NOH	C [auth A], D [auth B]	2'-deoxy-N-hydroxycytidine 5'-(dihydrogen phosphate) C9 H14 N3 O8 P YKOWBJJOJNGCAD-SHYZEUOFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.267 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.412	α = 90
b = 95.893	β = 103.81
c = 82.179	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data collection
CrysalisPro	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-18 
Deposition Author(s): Wilk, P., Jarmula, A., Rode, W.

Revision History  

• Version 1.0: 2015-02-18
  Type: Initial release
  
• Version 1.1: 2015-02-25
  Changes: Database references
• Version 1.2: 2015-06-17
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Refinement description