4F7W | pdb_00004f7w

Crystal structure of Klebsiella pneumoniae pantothenate kinase in complex with N-pentylpantothenamide

PDB DOI: https://doi.org/10.2210/pdb4F7W/pdb

Classification: TRANSFERASE, BIOSYNTHETIC PROTEIN
Organism(s): Klebsiella variicola 342
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-05-16 Released: 2013-04-10
Deposition Author(s): Li, B., Tempel, W., Smil, D., Bolshan, Y., Hong, B.S., Park, H.W., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.226 (Depositor), 0.233 (DCC)
R-Value Work:
0.185 (Depositor), 0.194 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structures of Klebsiella pneumoniae pantothenate kinase in complex with N-substituted pantothenamides.

Li, B., Tempel, W., Smil, D., Bolshan, Y., Schapira, M., Park, H.W.

(2013) Proteins 81: 1466-1472

PubMed: 23553820 Search on PubMed
DOI: https://doi.org/10.1002/prot.24290
Primary Citation Related Structures:
4F7W, 4GI7

PubMed Abstract:
N-Substituted pantothenamides are derivatives of pantothenate, the precursor in the biosynthesis of the essential metabolic cofactor coenzyme A (CoA). These compounds are substrates of pantothenate kinase (PanK) in the first step of CoA biosynthesis and possess antimicrobial activity against various pathogenic bacteria. Here we solved the crystal structure of the Klebsiella pneumoniae PanK (KpPanK) in complex with N-pentylpantothenamide (N5-Pan) to understand the molecular basis of its antimicrobial activity. The structure reveals a polar pocket interacting with the pantothenate moiety of N5-Pan and an aromatic pocket loosely protecting the pentyl tail, suggesting that the introduction of an aromatic ring to a new pantothenamide may enhance the compound's affinity to KpPanK. To test this idea, we synthesized N-pyridin-3-ylmethylpantothenamide (Np-Pan) and solved its co-crystal structure with KpPanK. The structure reveals two alternat conformations of the aromatic ring of Np-Pan bound at the aromatic pocket, providing the basis for further improvement of pantothenamide binding to KpPanK.

Organizational Affiliation

Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.

Macromolecule Content

Total Structure Weight: 313.12 kDa
Atom Count: 21,299
Modeled Residue Count: 2,459
Deposited Residue Count: 2,672
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pantothenate kinase	A B [auth C] C [auth B] D E A, B [auth C], C [auth B], D, E, F, G, H	334	Klebsiella variicola 342	Mutation(s): 0 Gene Names: coaA, KPK_5321 EC: 2.7.1.33
UniProt
Find proteins for B5XYG3 (Klebsiella variicola (strain 342)) Explore B5XYG3 Go to UniProtKB: B5XYG3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5XYG3
Sequence Annotations Expand
Reference Sequence

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 YA [auth G] SDF format, chain U [auth B] SDF format, chain PA [auth F] SDF format, chain NA [auth E] SDF format, chain L [auth C] SDF format, chain I [auth A] SDF format, chain GB [auth H] SDF format, chain DA [auth D] MOL2 format, chain YA [auth G] MOL2 format, chain U [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain NA [auth E] MOL2 format, chain L [auth C] MOL2 format, chain I [auth A] MOL2 format, chain GB [auth H] MOL2 format, chain DA [auth D] mmCIF format, chain YA [auth G] mmCIF format, chain U [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain NA [auth E] mmCIF format, chain L [auth C] mmCIF format, chain I [auth A] mmCIF format, chain GB [auth H] mmCIF format, chain DA [auth D]	DA [auth D] GB [auth H] I [auth A] L [auth C] NA [auth E] DA [auth D], GB [auth H], I [auth A], L [auth C], NA [auth E], PA [auth F], U [auth B], YA [auth G]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain DA [auth D] Focus chain GB [auth H] Focus chain I [auth A] Focus chain L [auth C] Focus chain NA [auth E] Focus chain PA [auth F] Focus chain U [auth B] Focus chain YA [auth G] Interactions & Density Focus chain DA [auth D] Focus chain GB [auth H] Focus chain I [auth A] Focus chain L [auth C] Focus chain NA [auth E] Focus chain PA [auth F] Focus chain U [auth B] Focus chain YA [auth G]
PN4 Query on PN4 Download:Ideal Coordinates CCD File SDF format, chain ZA [auth G] SDF format, chain V [auth B] SDF format, chain QA [auth F] SDF format, chain OA [auth E] SDF format, chain M [auth C] SDF format, chain J [auth A] SDF format, chain EA [auth D] MOL2 format, chain ZA [auth G] MOL2 format, chain V [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain OA [auth E] MOL2 format, chain M [auth C] MOL2 format, chain J [auth A] MOL2 format, chain EA [auth D] mmCIF format, chain ZA [auth G] mmCIF format, chain V [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain OA [auth E] mmCIF format, chain M [auth C] mmCIF format, chain J [auth A] mmCIF format, chain EA [auth D]	EA [auth D] J [auth A] M [auth C] OA [auth E] QA [auth F] EA [auth D], J [auth A], M [auth C], OA [auth E], QA [auth F], V [auth B], ZA [auth G]	(2R)-2,4-dihydroxy-3,3-dimethyl-N-[3-oxo-3-(pentylamino)propyl]butanamide C₁₄ H₂₈ N₂ O₄ HWNKKPMQPCHGBA-LBPRGKRZSA-N		Interactions Focus chain EA [auth D] Focus chain J [auth A] Focus chain M [auth C] Focus chain OA [auth E] Focus chain QA [auth F] Focus chain V [auth B] Focus chain ZA [auth G] Interactions & Density Focus chain EA [auth D] Focus chain J [auth A] Focus chain M [auth C] Focus chain OA [auth E] Focus chain QA [auth F] Focus chain V [auth B] Focus chain ZA [auth G]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain XA [auth F] SDF format, chain X [auth B] SDF format, chain WA [auth F] SDF format, chain W [auth B] SDF format, chain VA [auth F] SDF format, chain UA [auth F] SDF format, chain TA [auth F] SDF format, chain T [auth C] SDF format, chain SA [auth F] SDF format, chain S [auth C] SDF format, chain RA [auth F] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain MA [auth D] SDF format, chain LA [auth D] SDF format, chain KB [auth H] SDF format, chain KA [auth D] SDF format, chain K [auth A] SDF format, chain JB [auth H] SDF format, chain JA [auth D] SDF format, chain IB [auth H] SDF format, chain IA [auth D] SDF format, chain HB [auth H] SDF format, chain GA [auth D] SDF format, chain FB [auth G] SDF format, chain FA [auth D] SDF format, chain EB [auth G] SDF format, chain DB [auth G] SDF format, chain CB [auth G] SDF format, chain CA [auth B] SDF format, chain BB [auth G] SDF format, chain BA [auth B] SDF format, chain AB [auth G] SDF format, chain AA [auth B] MOL2 format, chain HA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain XA [auth F] MOL2 format, chain X [auth B] MOL2 format, chain WA [auth F] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain UA [auth F] MOL2 format, chain TA [auth F] MOL2 format, chain T [auth C] MOL2 format, chain SA [auth F] MOL2 format, chain S [auth C] MOL2 format, chain RA [auth F] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain KB [auth H] MOL2 format, chain KA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain JB [auth H] MOL2 format, chain JA [auth D] MOL2 format, chain IB [auth H] MOL2 format, chain IA [auth D] MOL2 format, chain HB [auth H] MOL2 format, chain GA [auth D] MOL2 format, chain FB [auth G] MOL2 format, chain FA [auth D] MOL2 format, chain EB [auth G] MOL2 format, chain DB [auth G] MOL2 format, chain CB [auth G] MOL2 format, chain CA [auth B] MOL2 format, chain BB [auth G] MOL2 format, chain BA [auth B] MOL2 format, chain AB [auth G] MOL2 format, chain AA [auth B] mmCIF format, chain HA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain XA [auth F] mmCIF format, chain X [auth B] mmCIF format, chain WA [auth F] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain UA [auth F] mmCIF format, chain TA [auth F] mmCIF format, chain T [auth C] mmCIF format, chain SA [auth F] mmCIF format, chain S [auth C] mmCIF format, chain RA [auth F] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain MA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain KB [auth H] mmCIF format, chain KA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain JB [auth H] mmCIF format, chain JA [auth D] mmCIF format, chain IB [auth H] mmCIF format, chain IA [auth D] mmCIF format, chain HB [auth H] mmCIF format, chain GA [auth D] mmCIF format, chain FB [auth G] mmCIF format, chain FA [auth D] mmCIF format, chain EB [auth G] mmCIF format, chain DB [auth G] mmCIF format, chain CB [auth G] mmCIF format, chain CA [auth B] mmCIF format, chain BB [auth G] mmCIF format, chain BA [auth B] mmCIF format, chain AB [auth G] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth G] BA [auth B] BB [auth G] CA [auth B] AA [auth B], AB [auth G], BA [auth B], BB [auth G], CA [auth B], CB [auth G], DB [auth G], EB [auth G], FA [auth D], FB [auth G], GA [auth D], HA [auth D], HB [auth H], IA [auth D], IB [auth H], JA [auth D], JB [auth H], K [auth A], KA [auth D], KB [auth H], LA [auth D], MA [auth D], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth C], RA [auth F], S [auth C], SA [auth F], T [auth C], TA [auth F], UA [auth F], VA [auth F], W [auth B], WA [auth F], X [auth B], XA [auth F], Y [auth B], Z [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain AA [auth B] Focus chain AB [auth G] Focus chain BA [auth B] Focus chain BB [auth G] Focus chain CA [auth B] Focus chain CB [auth G] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain FA [auth D] Focus chain FB [auth G] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain IA [auth D] Focus chain IB [auth H] Focus chain JA [auth D] Focus chain JB [auth H] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth H] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain RA [auth F] Focus chain S [auth C] Focus chain SA [auth F] Focus chain T [auth C] Focus chain TA [auth F] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain W [auth B] Focus chain WA [auth F] Focus chain X [auth B] Focus chain XA [auth F] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth G] Focus chain BA [auth B] Focus chain BB [auth G] Focus chain CA [auth B] Focus chain CB [auth G] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain FA [auth D] Focus chain FB [auth G] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain IA [auth D] Focus chain IB [auth H] Focus chain JA [auth D] Focus chain JB [auth H] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth H] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain RA [auth F] Focus chain S [auth C] Focus chain SA [auth F] Focus chain T [auth C] Focus chain TA [auth F] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain W [auth B] Focus chain WA [auth F] Focus chain X [auth B] Focus chain XA [auth F] Focus chain Y [auth B] Focus chain Z [auth B]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001043 (PN4) Query on PRD_001043	EA [auth D] J [auth A] M [auth C] OA [auth E] QA [auth F] EA [auth D], J [auth A], M [auth C], OA [auth E], QA [auth F], V [auth B], ZA [auth G]	N-pentylpantothenamide	Non-polymer / Antibiotic, Antimicrobial		Interactions Focus chain EA [auth D] Focus chain J [auth A] Focus chain M [auth C] Focus chain OA [auth E] Focus chain QA [auth F] Focus chain V [auth B] Focus chain ZA [auth G] Interactions & Density Focus chain EA [auth D] Focus chain J [auth A] Focus chain M [auth C] Focus chain OA [auth E] Focus chain QA [auth F] Focus chain V [auth B] Focus chain ZA [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.226 (Depositor), 0.233 (DCC)
R-Value Work: 0.185 (Depositor), 0.194 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.837	α = 90
b = 130.825	β = 90
c = 192.15	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-04-10

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2013-04-10
Type: Initial release
Version 1.1: 2013-04-17
Changes: Database references
Version 1.2: 2013-08-07
Changes: Database references
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations