6G2M | pdb_00006g2m

Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor PB-PAU

• PDB DOI: https://doi.org/10.2210/pdb6G2M/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-03-23 Released: 2018-07-11 
• Deposition Author(s): Pachl, P., Rezacova, P., Brynda, J.
• Funding Organization(s): Grant Agency of the Czech Republic, Czech Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.125 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.126 (Depositor) 

Starting Model: experimental

Literature

Structure-based optimization of bisphosphonate nucleoside inhibitors of human 5'(3')-deoxyribonucleotidases

Pachl, P., Simak, O., Budesinsky, M., Brynda, J., Rosenberg, I., Rezacova, P.

(2018) European J Org Chem 

• DOI: https://doi.org/10.1002/ejoc.201800515

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 Evidence: homology

Macromolecule Content

• Total Structure Weight: 24.27 kDa 
• Atom Count: 2,008 
• Modelled Residue Count: 197 
• Deposited Residue Count: 202 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'(3')-deoxyribonucleotidase, mitochondrial	A	202	Homo sapiens	Mutation(s): 0  Gene Names: NT5M, DNT2 EC: 3.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPB1 (Homo sapiens) Explore Q9NPB1  Go to UniProtKB:  Q9NPB1
PHAROS:  Q9NPB1 GTEx:  ENSG00000205309

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O84	F [auth A]	[(2~{R},4~{a}~{R},6~{R},7~{a}~{R})-6-[2,4-bis(oxidanylidene)-5-[(~{E})-3-phosphonoprop-1-enyl]pyrimidin-1-yl]-2-phenyl-4~{a},6,7,7~{a}-tetrahydro-4~{H}-furo[3,2-d][1,3]dioxin-2-yl]phosphonic acid C19 H22 N2 O11 P2 TZXVMSWLUKAZDT-PDBOZARJSA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME	B [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
EDO	G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	I [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.125 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.858	α = 90
b = 73.858	β = 90
c = 106.121	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-07-11 
Deposition Author(s): Pachl, P., Rezacova, P., Brynda, J.

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Funding Organization	Location	Grant Number
Grant Agency of the Czech Republic	Czech Republic	203-09-0820
Grant Agency of the Czech Republic	Czech Republic	15-05677S
Czech Science Foundation	Czech Republic	17-12703S

Revision History  

• Version 1.0: 2018-07-11
  Type: Initial release
  
• Version 1.1: 2019-02-06
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description