4KX5 | pdb_00004kx5

Cytosolic 5'-nucleotidase III complexed with cytidine 5'-monophosphate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.205 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.157 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 

Literature

Cytosolic 5'-nucleotidase III complexed with cytidine 5'-monophosphate

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

To be published.

Macromolecule Content 

  • Total Structure Weight: 35.13 kDa 
  • Atom Count: 2,715 
  • Modeled Residue Count: 291 
  • Deposited Residue Count: 297 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytosolic 5'-nucleotidase 3297Mus musculusMutation(s): 1 
Gene Names: Nt5c3
EC: 3.1.3.5 (PDB Primary Data), 3.1.3.91 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D020 (Mus musculus)
Explore Q9D020 
Go to UniProtKB:  Q9D020
IMPC:  MGI:1927186
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9D020
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C5P

Query on C5P


Download:Ideal Coordinates CCD File
B [auth A]CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
EPE

Query on EPE


Download:Ideal Coordinates CCD File
E [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
BME

Query on BME


Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]		BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
O [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.205 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.846α = 90
b = 46.846β = 90
c = 285.894γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2024-07-03
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description