4YIK | pdb_00004yik

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

• PDB DOI: https://doi.org/10.2210/pdb4YIK/pdb

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


• Deposited: 2015-03-02 Released: 2015-09-09 
• Deposition Author(s): Pachl, P., Rezacova, P., Brynda, J.
• Funding Organization(s): Grant Agency of the Czech Republic

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.176 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Structure-based design of a bisphosphonate 5'(3')-deoxyribonucleotidase inhibitor

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

(2015) Medchemcomm 6: 1635-1638

• DOI: https://doi.org/10.1039/C5MD00235D

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)

Macromolecule Content 

• Total Structure Weight: 24.81 kDa 
• Atom Count: 2,040 
• Modeled Residue Count: 201 
• Deposited Residue Count: 201 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'(3')-deoxyribonucleotidase, mitochondrial	A	201	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
2O2	G [auth A]	1-{2-deoxy-3,5-O-[phenyl(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-[(E)-2-phosphonoethenyl]pyrimidine-2,4(1H,3H)-dione C18 H20 N2 O11 P2 AYSYVLQGVXZPIY-OAIWFRFLSA-N
TRS	H [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	N [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C [auth A], D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.176 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.87	α = 90
b = 73.87	β = 90
c = 106.19	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-09-09 
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	--

Revision History  

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 2.0: 2017-09-06
  Changes: Atomic model, Author supporting evidence, Derived calculations
• Version 2.1: 2019-02-06
  Changes: Data collection, Database references
• Version 2.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description