4NB4 | pdb_00004nb4

Pantothenamide-bound Pantothenate kinase from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb4NB4/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus subsp. aureus MRSA252
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-10-22 Released: 2014-03-05
Deposition Author(s): Hughes, S.J., Antoshchenko, T., Smil, D., Park, H.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.284 (Depositor), 0.247 (DCC)
R-Value Work:
0.230 (Depositor)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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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 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: 257.8 kDa
Atom Count: 17,249
Modeled Residue Count: 2,113
Deposited Residue Count: 2,280
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type II pantothenate kinase	A, B, C, D, E A, B, C, D, E, F, G, H	285	Staphylococcus aureus subsp. aureus MRSA252	Mutation(s): 0 Gene Names: CoaA, coaW EC: 2.7.1.33
UniProt
Find proteins for Q6G7I0 (Staphylococcus aureus (strain MSSA476)) Explore Q6G7I0 Go to UniProtKB: Q6G7I0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6G7I0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SH3 Query on SH3 Download:Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain EA [auth H] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain X [auth F] SDF format, chain Y [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth F] mmCIF format, chain BA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain X [auth F] mmCIF format, chain Y [auth F]	BA [auth G] EA [auth H] J [auth A] K [auth A] P [auth C] BA [auth G], EA [auth H], J [auth A], K [auth A], P [auth C], Q [auth C], X [auth F], Y [auth F]	N-[2-(1,3-benzodioxol-5-yl)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide C₁₈ H₂₇ N₂ O₉ P OQCPPROGRWYIDC-INIZCTEOSA-N		Interactions Focus chain BA [auth G] Focus chain EA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain X [auth F] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain EA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain X [auth F] Focus chain Y [auth F]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain DA [auth H] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain U [auth E] SDF format, chain W [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain DA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F]	AA [auth G] DA [auth H] I [auth A] M [auth B] O [auth C] AA [auth G], DA [auth H], I [auth A], M [auth B], O [auth C], S [auth D], U [auth E], W [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain FA [auth H] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain Z [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain T [auth D] mmCIF format, chain V [auth E] mmCIF format, chain Z [auth F]	CA [auth G] FA [auth H] L [auth A] N [auth B] R [auth C] CA [auth G], FA [auth H], L [auth A], N [auth B], R [auth C], T [auth D], V [auth E], Z [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain FA [auth H] Focus chain L [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain FA [auth H] Focus chain L [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.284 (Depositor), 0.247 (DCC)
R-Value Work: 0.230 (Depositor)
R-Value Observed: 0.233 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.01	α = 90
b = 70.74	β = 90.64
c = 143.115	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-03-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-03-05
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