8HRV

dutpase of helicobacter pylori 26695

PDB DOI: https://doi.org/10.2210/pdb8HRV/pdb

Classification: HYDROLASE
Organism(s): Helicobacter pylori 26695
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-12-16 Released: 2024-01-17
Deposition Author(s): Kumari, K., Gourinath, S.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.181
R-Value Work: 0.145

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

dutpase of helicobacter pylori 26695

Kumari, K., Gourinath, S.

To be published.

Macromolecule Content

Total Structure Weight: 51.7 kDa
Atom Count: 3,622
Modelled Residue Count: 434
Deposited Residue Count: 456
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyuridine 5'-triphosphate nucleotidohydrolase	A, B, C	152	Helicobacter pylori 26695	Mutation(s): 0 Gene Names: dut, HP_0865 EC: 3.6.1.23
UniProt
Find proteins for O25536 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25536 Go to UniProtKB: O25536
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O25536
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DUP (Subject of Investigation/LOI) Query on DUP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C]	D [auth A], H [auth B], I [auth C]	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₃ P₃ XZLLMTSKYYYJLH-SHYZEUOFSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain J [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain J [auth C]	E [auth A], F [auth B], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain J [auth C]