6G2N | pdb_00006g2n

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

• PDB DOI: https://doi.org/10.2210/pdb6G2N/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: 1.40 Å
• R-Value Free: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.152 (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: 48.82 kDa 
• Atom Count: 3,506 
• Modeled Residue Count: 384 
• Deposited Residue Count: 410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'(3')-deoxyribonucleotidase, cytosolic type	A, B	205	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O84	D [auth A], F [auth B]	[(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
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A, B	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.877	α = 67.86
b = 47.231	β = 88.69
c = 61.795	γ = 77.37

Software Package:

Software Name	Purpose
XDS	data reduction
MOLREP	phasing
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: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary