6G2L

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

PDB DOI: https://doi.org/10.2210/pdb6G2L/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.150
R-Value Work: 0.122
R-Value Observed: 0.122

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 24.09 kDa
Atom Count: 2,023
Modelled Residue Count: 198
Deposited Residue Count: 202
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NPB1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EJ8 Query on EJ8 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	[(2~{R},4~{a}~{R},6~{R},7~{a}~{R})-6-[2,4-bis(oxidanylidene)-5-(phosphonomethylsulfanylmethyl)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 C₁₈ H₂₂ N₂ O₁₁ P₂ S KFRRWRABRKBEOD-ATNYBXOESA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.150
R-Value Work: 0.122
R-Value Observed: 0.122
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.797	α = 90
b = 73.797	β = 90
c = 106.632	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-07-11

Deposition Author(s):

Pachl, P.

Rezacova, P.

Brynda, J.

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 (Full details and data files)

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: Data collection, Database references, Derived calculations, Refinement description