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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ENGINEERED CONSTRUCT OF PHOSPHATIDYLINOSITOL 4 KINASE III BETA WITH A POTENT AND SELECTIVE INHIBITOR IN COMPLEX WITH GDP LOADED RAB11
 
Authors :  J. E. Burke, M. L. Fowler
Date :  19 Nov 15  (Deposition) - 24 Feb 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  B,E
Keywords :  Lipid Kinase, Gtpase Complex, Transferase-Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. U. Rutaganira, M. L. Fowler, J. A. Mcphail, M. A. Gelman, K. Nguyen, A. Xiong, G. L. Dornan, B. Tavshanjian, J. S. Glenn, K. M. Shokat, J. E. Burke
Design And Structural Characterization Of Potent And Selective Inhibitors Of Phosphatidylinositol 4 Kinase Iii Beta.
J. Med. Chem. V. 59 1830 2016
PubMed-ID: 26885694  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01311

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAB-11A
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPOPTG
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneRAB11A, RAB11
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRAB-11,YL8
 
Molecule 2 - PHOSPHATIDYLINOSITOL 4-KINASE BETA
    ChainsE
    EC Number2.7.1.67
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPOPTH
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GenePI4KB
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPTDINS 4-KINASE BETA,NPIK,PI4K92

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit BE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
15S81Ligand/Ion~{N}-[5-[3-[[(4-HYDROXYPHENYL)AMINO]-BIS(OXIDANYL)-$L^{4}-SULFANYL]-4-METHOXY-PHENYL]-4-METHYL-1,3-THIAZOL-2-YL]CYCLOPENTANECARBOXAMIDE
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:20 , GLY B:21 , VAL B:22 , GLY B:23 , LYS B:24 , SER B:25 , ASN B:26 , PHE B:36 , ASN B:37 , LEU B:38 , ASN B:124 , LYS B:125 , ASP B:127 , LEU B:128 , SER B:154 , ALA B:155 , LEU B:156binding site for residue GDP B 301
2AC2SOFTWAREHIS E:605 , LYS E:608 , ASN E:659binding site for residue SO4 E 1001
3AC3SOFTWARETYR E:183 , LYS E:195 , ARG E:232 , GLY E:233 , LYS E:235 , LEU E:236binding site for residue SO4 E 1002
4AC4SOFTWARELEU E:374 , PRO E:381 , ILE E:547 , LYS E:549 , TYR E:583 , ILE E:595 , PRO E:597 , VAL E:598 , ALA E:601 , GLY E:660 , ASN E:661 , LEU E:663 , ILE E:673binding site for residue 5S8 E 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EUQ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu E:348 -Pro E:349

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EUQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EUQ)

(-) Exons   (0, 0)

(no "Exon" information available for 5EUQ)

(-) 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 B from PDB  Type:PROTEIN  Length:155
                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.....hhhhhhhhhhh.........eeeeeeeee..eeeeeeeee...hhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5euq B   7 EYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESGVEFATRSIQVDGKTIKAQIWDTATSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIY 173
                                    16        26        36   ||   50        60       |78        88        98       108       118       128       138       148       158       168     
                                                            40|                     68|                                                                                                
                                                             45                      77                                                                                                

Chain E from PDB  Type:PROTEIN  Length:464
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh............eeeee.hhhhhee........eeeeeeeee......................hhhhhhhhhhhh........eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh..........eee.....eee.....eeehhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.........eeee....eee.............hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5euq E 128 SWLLRLFESKLFDISMAISYLYNSKEPGVQAYIGNRLFCFRNEDVDFYLPQLLNMYIHMDEDVGDAIKPYIVHRCRQSINFSLQCALLLGAYSSRGTKLRKLILSRLAPEREFIKSLMAIGKRLATLPTKEQKTQRLISELSLLNHKLPARVWLPTAGFDHHVVRVPHTQAVVLNSKDKAPYLIYVEVLECENFDTTSVPARIPPSAVALKEPWQEKVRRIREGSPYGHLPNWRLLSVIVKCGDDLRQELLAFQVLKQLQSIWEQERVPLWIKPYKILVISADSGMIEPVVNAVSIHQVKKQSQLSLLDYFLQEHGSYTTEAFLSAQRNFVQSCAGYCLVCYLLQVKDRHNGNILLDAEGHIIHIDFGFILSSSPKLTTEFVDVMGGLDGDMFNYYKMLMLQGLIAARKHMDKVVQIVEIMQQGSQLPCFHGSSTIRNLKERFHMSMTEEQLQLLVEQMVDGSM 782
                                   137       147       157       167       177       187       197       207       217   ||  237    || 310       320       330       340       350       360       370       380       390       400   ||  518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678    || 698       708       718       728       738       748       758       768       778    
                                                                                                                       221|       242|                                                                                               404|                                                                                                                                                                       683|                                                                                        
                                                                                                                        232        306                                                                                                513                                                                                                                                                                        694                                                                                        

   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  (0, 0)

(no "SCOP Domain" information available for 5EUQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EUQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EUQ)

(-) Gene Ontology  (73, 99)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Leu E:348 - Pro E:349   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PI4KB_HUMAN | Q9UBF82n73 4d0l 4d0m 4wae 4wag 5c46 5c4g 5fbl 5fbq 5fbr 5fbv 5fbw 5lx2 5nas
        RB11A_HUMAN | P624911oiv 1oiw 1oix 1yzk 2d7c 2gzd 2gzh 2hv8 4c4p 4d0l 4d0m 4lwz 4lx0 4uj3 4uj4 4uj5 5c46 5c4g 5ez5 5fbl 5fbq 5fbr 5fbv 5fbw 5jcz

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5EUQ)