6AN4 | pdb_00006an4

Crystal structure of Escherichia coli HPPK in complex with bisubstrate analogue inhibitor HP-39 (J1F)

PDB DOI: https://doi.org/10.2210/pdb6AN4/pdb

Classification: TRANSFERASE/INHIBITOR
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-08-12 Released: 2018-08-15
Deposition Author(s): Shaw, G.X., Shi, G., Ji, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.210 (Depositor), 0.210 (DCC)
R-Value Work:
0.200 (Depositor), 0.201 (DCC)
R-Value Observed:
0.200 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Bisubstrate analog inhibitors of HPPK: Transition state mimetics

Shaw, X.G., Shi, G., Ji, X.

To be published.

Macromolecule Content

Total Structure Weight: 18.7 kDa
Atom Count: 1,606
Modeled Residue Count: 151
Deposited Residue Count: 158
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase	A	158	Escherichia coli K-12	Mutation(s): 0 Gene Names: folK, b0142, JW0138 EC: 2.7.6.3
UniProt
Find proteins for P26281 (Escherichia coli (strain K12)) Explore P26281 Go to UniProtKB: P26281
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26281
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
J1F Query on J1F Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	((2-(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carboxamido)-N-(2-((((2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)amino)-2-oxoethyl)acetamido)methyl)phosphonic acid C₂₄ H₃₂ N₁₃ O₁₀ P IHZBIHWJVSGIOO-MDNHXVGFSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.210 (Depositor), 0.210 (DCC)
R-Value Work: 0.200 (Depositor), 0.201 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.778	α = 90
b = 48.092	β = 90
c = 77.043	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data processing
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-08-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-08-15
Type: Initial release
Version 1.1: 2023-08-30
Changes: Data collection, Database references, Structure summary

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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.