6AVP | pdb_00006avp

Staphylococcus aureus Type II pantothenate kinase in complex with ADP and pantothenate analog Phosphate-MeO-N5Pan

PDB DOI: https://doi.org/10.2210/pdb6AVP/pdb

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

Deposited: 2017-09-04 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: 2.30 Å
R-Value Free:
0.295 (Depositor), 0.290 (DCC)
R-Value Work:
0.245 (Depositor), 0.250 (DCC)
R-Value Observed:
0.247 (Depositor)

wwPDB Validation 3D Report Full Report

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: 118.87 kDa
Atom Count: 8,435
Modelled Residue Count: 1,048
Deposited Residue Count: 1,060
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type II pantothenate kinase	A, B, C, D	265	Staphylococcus aureus	Mutation(s): 0 Gene Names: coaW, ERS072840_01840, ERS073071_01656, ERS073583_01730, SAMEA2236422_02154, SAMEA2236459_02267, SAMEA2384700_01964, SAMEA2384800_02212, SAMEA2384856_02334, SAMEA2445640_02323 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FWC7
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 E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
N7E Query on N7E Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	F [auth A], I [auth B], L [auth C], O [auth D]	N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(5-methoxypentyl)-beta-alaninamide C₁₅ H₃₁ N₂ O₈ P FOBYDOXAQNKICH-ZDUSSCGKSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain P [auth D] SDF format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C]	G [auth A], J [auth B], M [auth C], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]