5KNQ

Crystal structure of Mycobacterium tuberculosis hypoxanthine guanine phosphoribosyltransferase in complex with [3S,4R]-(4-(Guanin-9-yl)pyrrolidin-3-yl)oxymethanephosphonic acid and pyrophosphate

PDB DOI: https://doi.org/10.2210/pdb5KNQ/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.237
R-Value Work: 0.187
R-Value Observed: 0.191

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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.

Macromolecule Content

Total Structure Weight: 94.1 kDa
Atom Count: 5,723
Modelled Residue Count: 726
Deposited Residue Count: 828
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WHQ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6W8 Query on 6W8 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain Q [auth D] SDF format, chain E [auth A] SDF format, chain M [auth C] MOL2 format, chain I [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain M [auth C] mmCIF format, chain I [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain M [auth C]	E [auth A], I [auth B], M [auth C], Q [auth D]	[(3~{S},4~{R})-4-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)pyrrolidin-3-yl]oxymethylphosphonic acid C₁₀ H₁₅ N₆ O₅ P LMOOKHOOULQCAZ-RITPCOANSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]
POP Query on POP Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D]	H [auth A], L [auth B], P [auth C], T [auth D]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain K [auth B] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain K [auth B] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain K [auth B] mmCIF format, chain R [auth D]	F [auth A] G [auth A] J [auth B] K [auth B] N [auth C] F [auth A], G [auth A], J [auth B], K [auth B], N [auth C], O [auth C], R [auth D], S [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
6W8	BindingDB: 5KNQ	Ki: min: 740, max: 8000 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.237
R-Value Work: 0.187
R-Value Observed: 0.191
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.262	α = 90
b = 85.507	β = 107.22
c = 81.468	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-09-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-09-20
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description