5KNY | pdb_00005kny

Crystal structure of Mycobacterium tuberculosis hypoxanthine guanine phosphoribosyltransferase in complex with (3-((3R,4R)-3-(Guanin-9-yl)-4-((S)-2-hydroxy-2-phosphonoethoxy)pyrrolidin-1-yl)-3-oxopropyl)phosphonic acid

• PDB DOI: https://doi.org/10.2210/pdb5KNY/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-06-28 Released: 2017-09-20 
• Deposition Author(s): Eng, W.S., Rejman, D., Keough, D.T., Guddat, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

Crystal structure of Mycobacterium tuberculosis hypoxanthine guanine phosphoribosyltransferase in complex with pyrrolidine nucleoside phosphonate

Eng, W.S., Rejman, D., Keough, D.T., Guddat, L.W.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 93.96 kDa 
• Atom Count: 5,698 
• Modeled Residue Count: 729 
• Deposited Residue Count: 828 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypoxanthine-guanine phosphoribosyltransferase	A, B, C, D	207	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: hpt, hprT, Rv3624c, MTCY15C10.28 EC: 2.4.2.8
UniProt
Find proteins for P9WHQ9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WHQ9  Go to UniProtKB:  P9WHQ9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YPG	E [auth A], G [auth B], I [auth C], K [auth D]	[3-[(3~{R},4~{R})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[(2~{S})-2-oxidanyl-2-phosphono-ethoxy]pyrrolidin-1-y l]-3-oxidanylidene-propyl]phosphonic acid C14 H22 N6 O10 P2 RBYFDIJTTUISNF-MRTMQBJTSA-N
MG	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
YPG	BindingDB:  5KNY	Ki: 60 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.523	α = 90
b = 86.075	β = 105.95
c = 79.824	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-20 
Deposition Author(s): Eng, W.S., Rejman, D., Keough, D.T., Guddat, L.W.

Revision History  

• Version 1.0: 2017-09-20
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Derived calculations, Structure summary