5KNX | pdb_00005knx

Crystal structure of E. coli hypoxanthine phosphoribosyltransferase in complexed with {[(2-[(Hypoxanthin-9H-yl)methyl]propane-1,3-diyl)bis(oxy)]bis- (methylene)}diphosphonic Acid

PDB DOI: https://doi.org/10.2210/pdb5KNX/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., Guddat, L.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.221 (Depositor), 0.190 (DCC)
R-Value Work:
0.182 (Depositor)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

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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: 42.19 kDa
Atom Count: 3,020
Modeled Residue Count: 349
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6WC Query on 6WC Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	[2-[(6-oxidanylidene-1~{H}-purin-9-yl)methyl]-3-(phosphonomethoxy)propoxy]methylphosphonic acid C₁₁ H₁₈ N₄ O₉ P₂ UAIJWVVEDWVBMI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.221 (Depositor), 0.190 (DCC)
R-Value Work: 0.182 (Depositor)
R-Value Observed: 0.184 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.38	α = 90
b = 85.38	β = 90
c = 167.475	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: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.