4NE2 | pdb_00004ne2

Pantothenamide-bound Pantothenate Kinase from Klebsiella pneumoniae

PDB DOI: https://doi.org/10.2210/pdb4NE2/pdb

Classification: TRANSFERASE
Organism(s): Klebsiella pneumoniae 342
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-10-28 Released: 2014-02-26
Deposition Author(s): Hughes, S.J., Antoshchenko, T., Kim, K.P., Smil, D., Park, H.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.214 (Depositor), 0.220 (DCC)
R-Value Work:
0.154 (Depositor), 0.160 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural characterization of a new N-substituted pantothenamide bound to pantothenate kinases from Klebsiella pneumoniae and Staphylococcus aureus.

Hughes, S.J., Antoshchenko, T., Kim, K.P., Smil, D., Park, H.W.

(2014) Proteins 82: 1542-1548

PubMed: 24470271 Search on PubMed
DOI: https://doi.org/10.1002/prot.24524
Primary Citation of Related Structures:
4NB4, 4NE2

PubMed Abstract:
Pantothenate kinase (PanK) is the rate-limiting enzyme in Coenzyme A biosynthesis, catalyzing the ATP-dependent phosphorylation of pantothenate. We solved the co-crystal structures of PanKs from Staphylococcus aureus (SaPanK) and Klebsiella pneumonia (KpPanK) with N-[2-(1,3-benzodioxol-5-yl)ethyl] pantothenamide (N354-Pan). Two different N354-Pan conformers interact with polar/nonpolar mixed residues in SaPanK and aromatic residues in KpPanK. Additionally, phosphorylated N354-Pan is found at the closed active site of SaPanK but not at the open active site of KpPanK, suggesting an exchange of the phosphorylated product with a new N354-Pan only in KpPanK. Together, pantothenamides conformational flexibility and binding pocket are two key considerations for selective compound design.

Organizational Affiliation

Department of Pharmacology, University of Toronto, Toronto, Ontario, M5G 1L7.

Macromolecule Content

Total Structure Weight: 78.56 kDa
Atom Count: 5,569
Modelled Residue Count: 605
Deposited Residue Count: 668
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pantothenate kinase	A, B	334	Klebsiella pneumoniae 342	Mutation(s): 0 Gene Names: coaA, KPK_5321, UUU_44690 EC: 2.7.1.33
UniProt
Find proteins for B5XYG3 (Klebsiella pneumoniae (strain 342)) Explore B5XYG3 Go to UniProtKB: B5XYG3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B5XYG3
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
SH2 Query on SH2 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	(R)-N-(3-((2-(benzo[d][1,3]dioxol-5-yl)ethyl)amino)-3-oxopropyl)-2,4-dihydroxy-3,3-dimethylbutanamide C₁₈ H₂₆ N₂ O₆ WTOXXQQUHIAOIP-INIZCTEOSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.214 (Depositor), 0.220 (DCC)
R-Value Work: 0.154 (Depositor), 0.160 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.765	α = 90
b = 180.366	β = 90
c = 181.488	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-02-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-02-26
Type: Initial release
Version 1.1: 2014-06-25
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description