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(-) Description

Title :  PANTOTHENAMIDE-BOUND PANTOTHENATE KINASE FROM KLEBSIELLA PNEUMONIAE
 
Authors :  S. J. Hughes, T. Antoshchenko, K. P. Kim, D. Smil, H. W. Park
Date :  28 Oct 13  (Deposition) - 26 Feb 14  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Protein-Substrate Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Hughes, T. Antoshchenko, K. P. Kim, D. Smil, H. W. Park
Structural Characterization Of A New N-Substituted Pantothenamide Bound To Pantothenate Kinases From Klebsiell Pneumoniae And Staphylococcus Aureus.
Proteins V. 82 1542 2014
PubMed-ID: 24470271  |  Reference-DOI: 10.1002/PROT.24524

(-) Compounds

Molecule 1 - PANTOTHENATE KINASE
    Chains: A, B
    EC Number: 2.7.1.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-MHL
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: COAA, KPK_5321, UUU_44690
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 507522
    Strain: 342
    Synonym: PANTOTHENIC ACID KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3SH22Ligand/Ion(R)-N-(3-((2-(BENZO[D][1,3]DIOXOL-5-YL)ETHYL)AMINO)-3-OXOPROPYL)-2,4-DIHYDROXY-3,3-DIMETHYLBUTANAMIDE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3SH22Ligand/Ion(R)-N-(3-((2-(BENZO[D][1,3]DIOXOL-5-YL)ETHYL)AMINO)-3-OXOPROPYL)-2,4-DIHYDROXY-3,3-DIMETHYLBUTANAMIDE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3SH22Ligand/Ion(R)-N-(3-((2-(BENZO[D][1,3]DIOXOL-5-YL)ETHYL)AMINO)-3-OXOPROPYL)-2,4-DIHYDROXY-3,3-DIMETHYLBUTANAMIDE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:43 , ASP A:45 , SER A:96 , ALA A:98 , VAL A:99 , GLY A:100 , LYS A:101 , SER A:102 , THR A:103 , ARG A:243 , LYS A:303 , HIS A:307 , MG A:403 , HOH A:546 , HOH A:569 , HOH A:574 , HOH A:581 , HOH A:582 , HOH A:585 , HOH A:612BINDING SITE FOR RESIDUE ADP A 401
2AC2SOFTWAREASP A:127 , GLY A:146 , TYR A:175 , HIS A:177 , TYR A:180 , LEU A:201 , TYR A:240 , ARG A:243 , PHE A:244 , PHE A:247 , PHE A:259 , ASN A:282BINDING SITE FOR RESIDUE SH2 A 402
3AC3SOFTWARESER A:102 , ADP A:401 , HOH A:581 , HOH A:582 , HOH A:583BINDING SITE FOR RESIDUE MG A 403
4AC4SOFTWAREASN B:43 , ASP B:45 , SER B:96 , ALA B:98 , VAL B:99 , GLY B:100 , LYS B:101 , SER B:102 , THR B:103 , ARG B:243 , LYS B:303 , HIS B:307 , MG B:403 , HOH B:518 , HOH B:566 , HOH B:574 , HOH B:575 , HOH B:580 , HOH B:587 , HOH B:588 , HOH B:590 , HOH B:671BINDING SITE FOR RESIDUE ADP B 401
5AC5SOFTWAREASP B:127 , LEU B:130 , GLY B:146 , TYR B:151 , TYR B:180 , TYR B:240 , ARG B:243 , PHE B:244 , PHE B:247 , PHE B:259 , ASN B:282 , HOH B:550 , HOH B:569 , HOH B:677BINDING SITE FOR RESIDUE SH2 B 402
6AC6SOFTWARESER B:102 , ADP B:401 , HOH B:587 , HOH B:588 , HOH B:589 , HOH B:590BINDING SITE FOR RESIDUE MG B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NE2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NE2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NE2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NE2)

(-) Exons   (0, 0)

(no "Exon" information available for 4NE2)

(-) Sequences/Alignments

Asymmetric 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:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4ne2a_ A: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeehhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee....hhhhhhhhhhhhhhhhhhhh.eeeee.hhhh.hhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eee..ee....ee.....eee....eeeee......hhhhh.......hhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ne2 A   8 LMTPYLQFNRHQWAALRTLTEDEITRLKGINEDLSLEEVAEIYLPLSRLLNFYISSNLRRQAVLEQFLGTNGQRIPYIISIAGSVAVGKSTTARVLQALLSRWPEHRHVELITTDGFLHPNSVLKERGLMKKKGFPQSYDMHRLVKFVSDLKSGVPQATAPVYSHLIYDVIPDGDKTVAQPDILILEGLNVLQSGMDYPHDPHHVFVSDFVDFSIYVDAPEELLKSWYINRFLKFREGAFTDPDSYFHNYAKLSKEEAVDIATSLWNEINLMNLKENILPTRERASLIMTKSANHSVNQVRLRK 316
                                    17      ||32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312    
                                           24|                                                                                                                                                                                                                                                                                              
                                            30                                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:301
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4ne2b_ B: automated matches                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeehhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee....hhhhhhhhhhhhhhhhhhhh.eeeee.hhhh.hhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eee..ee....ee.....eee....eeeee......hhhhh.......hhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ne2 B   9 MTPYLQFNRHQWAALRTEDEITRLKGINEDLSLEEVAEIYLPLSRLLNFYISSNLRRQAVLEQFLGTNGQRIPYIISIAGSVAVGKSTTARVLQALLSRWPEHRHVELITTDGFLHPNSVLKERGLMKKKGFPQSYDMHRLVKFVSDLKSGVPQATAPVYSHLIYDVIPDGDKTVAQPDILILEGLNVLQSGMDYPHDPHHVFVSDFVDFSIYVDAPEELLKSWYINRFLKFREGAFTDPDSYFHNYAKLSKEEAVDIATSLWNEINLMNLKENILPTRERASLIMTKSANHSVNQVRLRK 316
                                    18     || 35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315 
                                          24|                                                                                                                                                                                                                                                                                            
                                           32
   Legend:   → Mismatch (orange background)
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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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NE2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NE2)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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4nb4