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(-) Description

Title :  STAPHYLOCOCCUS AUREUS TYPE II PANTOTHENATE KINASE IN COMPLEX WITH A PANTOTHENATE ANALOG
 
Authors :  K. Mottaghi, B. Hong, W. Tempel, H. Park, Structural Genomics Consor (Sgc)
Date :  12 Aug 13  (Deposition) - 03 Sep 14  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pantothenate Kinase, Inhibitor, Antibacterial, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Hughes, L. Barnard, K. Mottaghi, W. Tempel, T. Antoshchenko, B. S. Hong, A. Allali-Hassani, D. Smil, M. Vedadi, E. Strauss, H. W. Par
Discovery Of Potent Pantothenamide Inhibitors Of Staphylococcus Aureus Pantothenate Kinase Through A Minimal Sar Study: Inhibition Is Due To Trapping Of The Product.
Acs Infect Dis V. 2 627 2016
PubMed-ID: 27759386  |  Reference-DOI: 10.1021/ACSINFECDIS.6B00090

(-) Compounds

Molecule 1 - TYPE II PANTOTHENATE KINASE
    Chains: A, B
    EC Number: 2.7.1.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-V2R-TR
    Expression System Taxid: 562
    Gene: COAW, MW2054
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 196620
    Strain: MW2
    Synonym: PANK-II, PANTOTHENIC ACID KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 33)

Asymmetric/Biological Unit (4, 33)
No.NameCountTypeFull Name
12GH2Ligand/IonN~3~-[(2R)-2-HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY)BUTANOYL]-N-PENTYL-BETA-ALANINAMIDE
2ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
3PO47Ligand/IonPHOSPHATE ION
4UNX22Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:70 , PHE A:71 , GLY A:98 , THR A:99 , GLY A:100 , THR A:101 , SER A:102 , ARG A:113 , GLY A:116 , ILE A:117 , ADP A:302 , HOH A:412 , HOH A:425 , HOH A:440 , HOH A:495 , THR B:172 , ALA B:173 , GLU B:202 , TYR B:240BINDING SITE FOR RESIDUE 2GH A 301
02AC2SOFTWAREGLY A:8 , GLY A:9 , THR A:10 , LEU A:11 , LYS A:13 , LEU A:28 , GLY A:98 , THR A:99 , GLY A:121 , GLY A:122 , GLN A:125 , TYR A:137 , GLY A:224 , SER A:225 , SER A:226 , 2GH A:301 , HOH A:401 , HOH A:435 , HOH A:440 , HOH A:457 , HOH A:458BINDING SITE FOR RESIDUE ADP A 302
03AC3SOFTWAREARG A:113 , VAL A:114 , GLY A:115 , HOH A:495 , ARG B:213 , ARG B:244 , PO4 B:305BINDING SITE FOR RESIDUE PO4 A 303
04AC4SOFTWAREASP A:88 , LEU A:89 , ALA A:90 , ASP A:91 , ASN A:219BINDING SITE FOR RESIDUE PO4 A 304
05AC5SOFTWARETHR A:172 , ALA A:173 , GLU A:202 , TYR A:240 , GLU B:70 , PHE B:71 , GLY B:98 , THR B:99 , GLY B:100 , THR B:101 , SER B:102 , ARG B:113 , GLY B:116 , ILE B:117 , ADP B:302 , HOH B:404 , HOH B:413 , HOH B:430 , HOH B:442BINDING SITE FOR RESIDUE 2GH B 301
06AC6SOFTWAREGLY B:8 , GLY B:9 , THR B:10 , LEU B:11 , LYS B:13 , GLY B:98 , THR B:99 , GLY B:121 , GLY B:122 , GLN B:125 , TYR B:137 , GLY B:224 , SER B:225 , SER B:226 , 2GH B:301 , HOH B:412 , HOH B:413 , HOH B:445 , HOH B:476BINDING SITE FOR RESIDUE ADP B 302
07AC7SOFTWAREHIS B:228 , ASN B:229 , ARG B:234 , TYR B:250 , PO4 B:311BINDING SITE FOR RESIDUE PO4 B 303
08AC8SOFTWAREARG A:112 , ARG B:213 , ARG B:244BINDING SITE FOR RESIDUE PO4 B 304
09AC9SOFTWAREPO4 A:303 , PRO B:168 , HOH B:457BINDING SITE FOR RESIDUE PO4 B 305
10BC1SOFTWAREHIS B:228 , ASN B:229 , PO4 B:303BINDING SITE FOR RESIDUE PO4 B 311
11BC2SOFTWARETHR B:26 , HIS B:228 , PHE B:256BINDING SITE FOR RESIDUE PO4 B 312

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M7Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4M7Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M7Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M7Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4M7Y)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeeeee..eeeeeeee..hhhhhhhhhh.....eeeee..hhhhhhhhh....ee.hhhhhhhhhhhhhhhhh......eeeeee...eeeeee....eeeeeee..hhhhhhhhhhhhhh..hhhhhhhhhh........eehhhhh...........eee...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhh.hhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m7y A   1 MKVGIDAGGTLIKIVQEQDNQRTFKTELTKNIDQVVEWLNQQQIEKLCLTGGNAGVIAENINIPAQIFVEFDAASQGLGILLKEQGHDLADYIFANVGTGTSLHYFDGQSQRRVGGIGTGGGMIQGLGYLLSQITDYKQLTDMAQHGDRNTIDLKVRHIYKDTEPPIPGDLTAANFGHVLHHLDADFTPSNKLAAVIGVVGEVVTTMAITVAREFKTENIVYIGSSFHNNALLRKVVEDYTVLRGCKPYYVENGAFSGAIGALYLE 266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      


Chain B from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeeeee..eeeeeeee..hhhhhhhhhhhh...eeeee..hhhhhhhhh....ee.hhhhhhhhhhhhhhhhh......eeeeee...eeeeee....eeeeeee..hhhhhhhhhhhhhh..hhhhhhhhhh........eehhhhh...........eee...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhh.hhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m7y B   1 MKVGIDAGGTLIKIVQEQDNQRTFKTELTKNIDQVVEWLNQQQIEKLCLTGGNAGVIAENINIPAQIFVEFDAASQGLGILLKEQGHDLADYIFANVGTGTSLHYFDGQSQRRVGGIGTGGGMIQGLGYLLSQITDYKQLTDMAQHGDRNTIDLKVRHIYKDTEPPIPGDLTAANFGHVLHHLDADFTPSNKLAAVIGVVGEVVTTMAITVAREFKTENIVYIGSSFHNNALLRKVVEDYTVLRGCKPYYVENGAFSGAIGALYLE 266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4M7Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M7Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M7Y)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        COAW_STAAW | Q8NVG0: 4m7x 5elz 5jic

(-) Related Entries Specified in the PDB File

4m7x