4KX3 | pdb_00004kx3

Structure of murine cytosolic 5'-nucleotidase III complexed with thymidine monophosphate

• PDB DOI: https://doi.org/10.2210/pdb4KX3/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-05-24 Released: 2013-06-05 
• Deposition Author(s): Bitto, E., Bingman, C.A., Grobosky, C.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.216 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Structure of murine cytosolic 5'-nucleotidase III complexed with thymidine monophosphate

Bitto, E., Bingman, C.A., Grobosky, C.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 34.77 kDa 
• Atom Count: 2,645 
• Modeled Residue Count: 291 
• Deposited Residue Count: 297 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 1 of Cytosolic 5'-nucleotidase 3A	A	297	Mus musculus	Mutation(s): 2  Gene Names: Nt5c3a, Nt5c3 EC: 3.1.3.5 (PDB Primary Data), 3.1.3.91 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D020 (Mus musculus) Explore Q9D020  Go to UniProtKB:  Q9D020
IMPC:  MGI:1927186

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TMP	B [auth A]	THYMIDINE-5'-PHOSPHATE C10 H15 N2 O8 P GYOZYWVXFNDGLU-XLPZGREQSA-N
EPE	G [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.216 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.872	α = 90
b = 46.872	β = 90
c = 285.873	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-05 
Deposition Author(s): Bitto, E., Bingman, C.A., Grobosky, C.L.

Revision History  

• Version 1.0: 2013-06-05
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2025-02-12
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary