4YIH | pdb_00004yih

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

• PDB DOI: https://doi.org/10.2210/pdb4YIH/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: 1.82 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.187 (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: 46.95 kDa 
• Atom Count: 3,350 
• Modelled Residue Count: 379 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'(3')-deoxyribonucleotidase, cytosolic type	A, B	195	Homo sapiens	Mutation(s): 0  Gene Names: NT5C, DNT1, UMPH2 EC: 3.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TCD5 (Homo sapiens) Explore Q8TCD5  Go to UniProtKB:  Q8TCD5
PHAROS:  Q8TCD5 GTEx:  ENSG00000125458

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2O2	E [auth A], I [auth B]	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
PO4	D [auth A], H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.818	α = 111.18
b = 46.451	β = 88.16
c = 61.738	γ = 104.7

Software Package:

Software Name	Purpose
MOLREP	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
XDS	data scaling

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	15-05677S

Revision History  

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 2.0: 2017-09-06
  Changes: Advisory, 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, Derived calculations, Refinement description