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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.228 (Depositor), 0.231 (DCC)
R-Value Work:
0.185 (Depositor), 0.192 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 46.95 kDa
Atom Count: 3,350
Modeled Residue Count: 379
Deposited Residue Count: 390
Unique protein chains: 1

Macromolecules

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| 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: 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TCD5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2O2 Query on 2O2 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	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		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.228 (Depositor), 0.231 (DCC)
R-Value Work: 0.185 (Depositor), 0.192 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-09-09

Deposition Author(s):

Pachl, P.

Rezacova, P.

Brynda, J.

Funding Organization	Location	Grant Number
Grant Agency of the Czech Republic	Czech Republic	15-05677S

Revision History (Full details and data files)

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