4L57

High resolutin structure of human cytosolic 5'(3')-deoxyribonucleotidase

PDB DOI: https://doi.org/10.2210/pdb4L57/pdb

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

Deposited: 2013-06-10 Released: 2014-02-12
Deposition Author(s): Pachl, P., Brynda, J., Rezacova, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.08 ?
R-Value Free: 0.183
R-Value Work: 0.144
R-Value Observed: 0.144

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors.

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

(2014) Acta Crystallogr D Biol Crystallogr 70: 461-470

PubMed: 24531480 Search on PubMed
DOI: https://doi.org/10.1107/S1399004713030502
Primary Citation of Related Structures:
4L57, 4L6A

PubMed Abstract:
The human 5'(3')-deoxyribonucleotidases catalyze the dephosphorylation of deoxyribonucleoside monophosphates to the corresponding deoxyribonucleosides and thus help to maintain the balance between pools of nucleosides and nucleotides. Here, the structures of human cytosolic deoxyribonucleotidase (cdN) at atomic resolution (1.08??) and mitochondrial deoxyribonucleotidase (mdN) at near-atomic resolution (1.4??) are reported. The attainment of an atomic resolution structure allowed interatomic distances to be used to assess the probable protonation state of the phosphate anion and the side chains in the enzyme active site. A detailed comparison of the cdN and mdN active sites allowed the design of a cdN-specific inhibitor.

Organizational Affiliation

Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 37 Prague 6, Czech Republic.

Macromolecule Content

Total Structure Weight: 46.42 kDa
Atom Count: 3,845
Modelled Residue Count: 384
Deposited Residue Count: 390
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, cytosolic type	A, B	195	Homo sapiens	Mutation(s): 0 Gene Names: DNT1, NT5C, 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8TCD5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain L [auth B]	D [auth A], L [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain L [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain K [auth B]	C [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.08 ?
R-Value Free: 0.183
R-Value Work: 0.144
R-Value Observed: 0.144
Space Group: P 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 39.128	α = 68.16
b = 46.493	β = 81.47
c = 61.409	γ = 75.28

Software Package:

Software Name	Purpose
SHELX	refinement
PDB_EXTRACT	data extraction
SHELXL	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-02-12

Deposition Author(s):

Pachl, P.

Brynda, J.

Rezacova, P.

Revision History (Full details and data files)

Version 1.0: 2014-02-12
Type: Initial release
Version 1.1: 2014-03-19
Changes: Refinement description
Version 1.2: 2018-04-18
Changes: Data collection, Database references
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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Help and Resources

4L57

High resolutin structure of human cytosolic 5'(3')-deoxyribonucleotidase

Structures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)