5WRN | pdb_00005wrn

Human thymidylate synthase complexed with dCMP

• PDB DOI: https://doi.org/10.2210/pdb5WRN/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-12-02 Released: 2016-12-14 
• Deposition Author(s): Chen, D., Nordlund, P.
• Funding Organization(s): Nanyang Technological University

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.247 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.188 (Depositor) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Human thymidylate synthase complexed with dCMP

Almqvist, H., Axelsson, H., Jafari, R., Chen, D., Mateus, A., Haraldsson, M., Larsson, A., Martinez Molina, D., Artursson, P., Lundback, T., Nordlund, P.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 200.85 kDa 
• Atom Count: 14,115 
• Modeled Residue Count: 1,697 
• Deposited Residue Count: 1,734 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A [auth B], B [auth A], C, D, E, F	289	Homo sapiens	Mutation(s): 0  Gene Names: TYMS, TS, OK/SW-cl.29 EC: 2.1.1.45
UniProt & NIH Common Fund Data Resources
Find proteins for P04818 (Homo sapiens) Explore P04818  Go to UniProtKB:  P04818
PHAROS:  P04818 GTEx:  ENSG00000176890

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCM	G [auth B], H [auth A], I [auth C], J [auth D], K [auth E], L [auth F]	2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE C9 H14 N3 O7 P NCMVOABPESMRCP-SHYZEUOFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.247 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.188 (Depositor) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.096	α = 90
b = 110.096	β = 90
c = 317.268	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing
HKL	data reduction
HKL	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Chen, D., Nordlund, P.

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Funding Organization	Location	Grant Number
Nanyang Technological University	Singapore	M060080004.70301200

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2024-05-29
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description