3EHW

Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site

PDB DOI: https://doi.org/10.2210/pdb3EHW/pdb

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

Deposited: 2008-09-15 Released: 2008-09-30
Deposition Author(s): Takacs, E., Barabas, O., Vertessy, B.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 ?
R-Value Free: 0.199
R-Value Work: 0.158
R-Value Observed: 0.160

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site

Takacs, E., Barabas, O., Vertessy, B.G.

To be published.

Macromolecule Content

Total Structure Weight: 109.62 kDa
Atom Count: 7,277
Modelled Residue Count: 841
Deposited Residue Count: 984
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dUTP pyrophosphatase	A B C D [auth X] E [auth Y] A, B, C, D [auth X], E [auth Y], F [auth Z]	164	Homo sapiens	Mutation(s): 0 Gene Names: DUT EC: 3.6.1.23
UniProt & NIH Common Fund Data Resources
Find proteins for P33316 (Homo sapiens) Explore P33316 Go to UniProtKB: P33316
PHAROS: P33316 GTEx: ENSG00000128951
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33316
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DUP Query on DUP Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain R [auth Y] SDF format, chain T [auth Z] SDF format, chain H [auth A] SDF format, chain O [auth X] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain R [auth Y] MOL2 format, chain T [auth Z] MOL2 format, chain H [auth A] MOL2 format, chain O [auth X] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain R [auth Y] mmCIF format, chain T [auth Z] mmCIF format, chain H [auth A] mmCIF format, chain O [auth X]	H [auth A] K [auth B] L [auth C] O [auth X] R [auth Y] H [auth A], K [auth B], L [auth C], O [auth X], R [auth Y], T [auth Z]	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₃ P₃ XZLLMTSKYYYJLH-SHYZEUOFSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain O [auth X] Focus chain R [auth Y] Focus chain T [auth Z] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain O [auth X] Focus chain R [auth Y] Focus chain T [auth Z]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth X] SDF format, chain P [auth X] SDF format, chain Q [auth Y] SDF format, chain S [auth Z] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth X] MOL2 format, chain P [auth X] MOL2 format, chain Q [auth Y] MOL2 format, chain S [auth Z] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth X] mmCIF format, chain P [auth X] mmCIF format, chain Q [auth Y] mmCIF format, chain S [auth Z]	G [auth A] I [auth A] J [auth B] M [auth C] N [auth X] G [auth A], I [auth A], J [auth B], M [auth C], N [auth X], P [auth X], Q [auth Y], S [auth Z]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth X] Focus chain P [auth X] Focus chain Q [auth Y] Focus chain S [auth Z] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth X] Focus chain P [auth X] Focus chain Q [auth Y] Focus chain S [auth Z]

Binding Affinity Annotations
ID	Source	Binding Affinity
DUP	PDBBind: 3EHW	IC50: 1.52e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 ?
R-Value Free: 0.199
R-Value Work: 0.158
R-Value Observed: 0.160
Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 65.446	α = 90
b = 87.16	β = 90.09
c = 70.608	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-09-30

Deposition Author(s):

Takacs, E.

Barabas, O.

Vertessy, B.G.

Revision History (Full details and data files)

Version 1.0: 2008-09-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2012-03-07
Changes: Database references
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-06
Changes: Structure summary

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Help and Resources

3EHW

Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site

Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)