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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHATIDYL INOSITOL 4-KINASE II ALPHA IN COMPLEX WITH NUCLEOTIDE ANALOG
 
Authors :  M. Klima, E. Boura
Date :  19 Feb 15  (Deposition) - 15 Jul 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.58
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase, Complex, Inhibitor, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Klima, A. Baumlova, D. Chalupska, H. Hrebabecky, M. Dejmek, R. Nencka, E. Boura
The High-Resolution Crystal Structure Of Phosphatidylinositol 4-Kinase Ii Beta And The Crystal Structure Of Phosphatidylinositol 4-Kinase Ii Alpha Containing A Nucleoside Analogue Provide A Structural Basis For Isoform-Specific Inhibitor Design.
Acta Crystallogr. , Sect. D V. 71 1555 2015
PubMed-ID: 26143926  |  Reference-DOI: 10.1107/S1399004715009505

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 4-KINASE TYPE 2-ALPHA,LYSOZYME, PHOSPHATIDYLINOSITOL 4-KINASE TYPE 2-ALPHA
    Chains: A
    EC Number: 2.7.1.67, 3.2.1.17, 2.7.1.67
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PRSFD
    Expression System Strain: STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PI4K2A, T4TP126
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS, ENTEROBACTERIA PHAGE T4
    Organism Taxid: 9606, 10665
    Synonym: PHOSPHATIDYLINOSITOL 4-KINASE TYPE II-ALPHA, PHOSPHATIDYLINOSITOL 4-KINASE TYPE II-ALPHA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2M591Ligand/Ion[(1S,3S,4S)-3-(6-AMINO-9H-PURIN-9-YL)BICYCLO[2.2.1]HEPT-1-YL]METHANOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:132 , GLN A:261 , LEU A:262 , PHE A:263 , VAL A:264 , ILE A:345 , ASP A:346 , HOH A:1302binding site for residue M59 A 1201
2AC2SOFTWARETRP A:359 , ARG A:360 , PRO A:363 , PHE A:364 , ALA A:367 , TRP A:368 , VAL A:444 , GLN A:445binding site for residue ADP A 1202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YC4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:1166 -Gly A:180

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YC4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YC4)

(-) Exons   (0, 0)

(no "Exon" information available for 4YC4)

(-) 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:486
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh....ee........eeee.....eeeeeee.hhh.....hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.....eeee..eeee...hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhh..........hhhhhhhhhhhhhhhhh......eeeeee.......hhhhhhhh........eeeeeee.....eehhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh........eeeee..........eeeee...................hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4yc4 A  101 RNEFPEDPEFEAVVRQAELAIERCIFPERIYQGSSGSYFVKDPQGRIIAVFKPKNEEPYGHLNPKWTKWLQKGTGNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNLGRDCLVLNQGYLSEAGASLVDQKLELNIVPRTKVVYLASETFNYSAIDRVKSRGRIGLPPKVGSFQLFVEGYKDADYWLRRFEAEPLPENTNRQLLLQFERLVVLDYIIRNTDRGNDNWLIKYDDWVVVKEPVIKVAAIDNGLAFPLKHPDSWRAYPFYWAWLPQAKVPFSQEIKDLILPKISDPNFVKDLEEDLYELFKKDPGFDRGQFHKQIAVMRGQILNLTQALKDNKSPLHLVQMPPVIVETA  454
                                   110       120       130       140       150       160       170 ||   1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158       181       191       201       211       221       231 ||    257       267       277       287       297       307       317 ||    338       348       358       368       378       388       398       408       418       428       438       448      
                                                                                                 172|                                                                                                                                                                 1166|                                                  233|                                                                  319|                                                                                                                           
                                                                                                 1001                                                                                                                                                                   180                                                   250                                                                   331
   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 4YC4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YC4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YC4)

(-) Gene Ontology  (50, 50)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        D9IEF7_BPT4 | D9IEF7: 4s0w 5ndd 5ndz 5t1a 5v83 5v86 5v88 5vba 5xez 5xf1
        P4K2A_HUMAN | Q9BTU6: 4hnd 4hne 4pla 5eut 5i0n
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(-) Related Entries Specified in the PDB File

4pla 4PLA CONTAINS THE SAME PROTEIN COMPLEXED WITH ATP