6AN6 | pdb_00006an6

Crystal structure of Escherichia coli HPPK in complex with bisubstrate analogue inhibitor HP-72

PDB DOI: https://doi.org/10.2210/pdb6AN6/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: 2.30 Å
R-Value Free:
0.257 (Depositor), 0.257 (DCC)
R-Value Work:
0.216 (Depositor), 0.221 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Bisubstrate analogue inhibitors of HPPK: Transition state mimetics

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

To be published.

Macromolecule Content

Total Structure Weight: 37.3 kDa
Atom Count: 2,782
Modeled Residue Count: 316
Deposited Residue Count: 316
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, B	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
J1I Query on J1I Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	5'-S-{2-[{2-[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carbonyl)amino]ethyl}(phosphonomethyl)amino]ethyl}-5'-thioadenosine C₂₄ H₃₅ N₁₂ O₈ P S LNONYTMYGAJODO-HUYKWJOFSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.257 (Depositor), 0.257 (DCC)
R-Value Work: 0.216 (Depositor), 0.221 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.67	α = 90
b = 52.924	β = 103.42
c = 77.43	γ = 90

Software Package:

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

Structure Validation

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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
Version 1.2: 2023-10-04
Changes: Refinement description

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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.