6AWG | pdb_00006awg

Staphylococcus aureus Type II pantothenate kinase in complex with nucleotides and pantothenate analog Deoxy-N190Pan

PDB DOI: https://doi.org/10.2210/pdb6AWG/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-09-05 Released: 2018-09-12
Deposition Author(s): Chen, Y., Antoshchenko, T., Strauss, E., Barnard, L., Huang, Y.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.267 (Depositor), 0.270 (DCC)
R-Value Work:
0.192 (Depositor), 0.199 (DCC)
R-Value Observed:
0.196 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Structure-based identification of uncompetitive inhibitors for Staphylococcus aureus pantothenate kinase.

Chen, Y., Antoshchenko, T., Strauss, E., Barnard, L., Huang, Y.H.

To be published.

Macromolecule Content

Total Structure Weight: 119.21 kDa
Atom Count: 8,653
Modeled Residue Count: 1,061
Deposited Residue Count: 1,064
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type II pantothenate kinase	A, B, C, D	266	Staphylococcus aureus	Mutation(s): 0 Gene Names: coaW, AYM28_11860, AYM37_11860, ERS072738_01917, ERS074020_01878, HMPREF3211_02599 EC: 2.7.1.33
UniProt
Find proteins for Q2FWC7 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FWC7 Go to UniProtKB: Q2FWC7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2FWC7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth C] mmCIF format, chain E [auth A] mmCIF format, chain I [auth C]	E [auth A], I [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth C]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain G [auth B] MOL2 format, chain K [auth D] MOL2 format, chain G [auth B] mmCIF format, chain K [auth D] mmCIF format, chain G [auth B]	G [auth B], K [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain G [auth B] Focus chain K [auth D] Interactions & Density Focus chain G [auth B] Focus chain K [auth D]
C0G Query on C0G Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	(2R)-N-(3-{[(2H-1,3-benzodioxol-5-yl)methyl]amino}-3-oxopropyl)-2-hydroxy-3,3-dimethylbutanamide C₁₇ H₂₄ N₂ O₅ CABNSQJZPOAZEV-HNNXBMFYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.267 (Depositor), 0.270 (DCC)
R-Value Work: 0.192 (Depositor), 0.199 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.651	α = 90
b = 57.171	β = 100.24
c = 134.536	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-09-12

Deposition Author(s):

Antoshchenko, T.

Revision History (Full details and data files)

Version 1.0: 2018-09-12
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references

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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.