5KNS | pdb_00005kns

E coli hypoxanthine guanine phosphoribosyltransferase in complexed with 9-[(N-phosphonoethyl-N-phosphonoethoxyethyl)-2-aminoethyl]hypoxanthine

PDB DOI: https://doi.org/10.2210/pdb5KNS/pdb

Classification: TRANSFERASE/INHIBITOR
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-06-28 Released: 2017-07-19
Deposition Author(s): Eng, W.S., Keough, D.T., Hockova, D., Janeba, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free:
0.209 (Depositor), 0.215 (DCC)
R-Value Work:
0.155 (Depositor), 0.165 (DCC)
R-Value Observed:
0.161 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structures of Acyclic Nucleoside Phosphonates in Complex with Escherichia coli Hypoxanthine Phosphoribosyltransferase

Eng, W.S., Hockova, D., Spacek, P., Baszczynski, O., Janeba, Z., Naesens, L., Keough, D.T., Guddat, L.W.

(2016) ChemistrySelect 1: 6267-6276

DOI: https://doi.org/10.1002/slct.201601679

Macromolecule Content

Total Structure Weight: 42.69 kDa
Atom Count: 3,006
Modeled Residue Count: 342
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypoxanthine-guanine phosphoribosyltransferase	A, B	182	Escherichia coli	Mutation(s): 0 Gene Names: hpt, ACN002_0124 EC: 2.4.2.8
UniProt
Find proteins for P0A9M2 (Escherichia coli (strain K12)) Explore P0A9M2 Go to UniProtKB: P0A9M2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A9M2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3L7 Query on 3L7 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	(2-{[2-(6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl](2-{[(E)-2-phosphonoethenyl]oxy}ethyl)amino}ethyl)phosphonic acid C₁₃ H₂₁ N₅ O₈ P₂ SGNFOZIWXPTVIN-SOFGYWHQSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.209 (Depositor), 0.215 (DCC)
R-Value Work: 0.155 (Depositor), 0.165 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.411	α = 90
b = 84.411	β = 90
c = 167.14	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-07-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-07-19
Type: Initial release
Version 1.1: 2024-03-06
Changes: Advisory, Data collection, Database references, Derived calculations

5KNS | pdb_00005kns

E coli hypoxanthine guanine phosphoribosyltransferase in complexed with 9-[(N-phosphonoethyl-N-phosphonoethoxyethyl)-2-aminoethyl]hypoxanthine

Literature

Crystal Structures of Acyclic Nucleoside Phosphonates in Complex with Escherichia coli Hypoxanthine Phosphoribosyltransferase

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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