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(-) Description

Title :  CRYSTAL STRUCTURE OF PI3KALPHA IN COMPLEX WITH FRAGMENTS 6 AND 24
 
Authors :  S. B. Gabelli, B. Vogelstein, M. S. Miller, L. M. Amzel
Date :  08 Aug 16  (Deposition) - 15 Feb 17  (Release) - 15 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.41
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lipid Kinase, Phosphoinositide, 3-Kinase, Signaling, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Miller, S. Maheshwari, F. M. Mcrobb, K. W. Kinzler, L. M. Amzel, B. Vogelstein, S. B. Gabelli
Identification Of Allosteric Binding Sites For Pi3K Alpha Oncogenic Mutant Specific Inhibitor Design.
Bioorg. Med. Chem. V. 25 1481 2017
PubMed-ID: 28129991  |  Reference-DOI: 10.1016/J.BMC.2017.01.012

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT ALPHA ISOFORM
    Chains: A
    EC Number: 2.7.1.153, 2.7.11.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBAC HT-A
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: PIK3CA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PTDINS-3-KINASE SUBUNIT ALPHA,PHOSPHATIDYLINOSITOL 4,5- BISPHOSPHATE 3-KINASE 110 KDA CATALYTIC SUBUNIT ALPHA,P110ALPHA, PHOSPHOINOSITIDE-3-KINASE CATALYTIC ALPHA POLYPEPTIDE, SERINE/THREONINE PROTEIN KINASE PIK3CA
 
Molecule 2 - PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT ALPHA
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBAC HT-A
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: PIK3R1, GRB1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PTDINS-3-KINASE REGULATORY SUBUNIT ALPHA, PHOSPHATIDYLINOSITOL 3-KINASE 85 KDA REGULATORY SUBUNIT ALPHA,PTDINS- 3-KINASE REGULATORY SUBUNIT P85-ALPHA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
170V2Ligand/Ion2-METHYLCYCLOHEXANE-1,3-DIONE
270W2Ligand/IonTERT-BUTYL 4-AMINOPIPERIDINE-1-CARBOXYLATE
3CL1Ligand/IonCHLORIDE ION
4SEP2Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:630binding site for residue 70W A 1101
2AC2SOFTWAREASP A:84 , ARG A:115 , ARG A:704 , GLU A:707binding site for residue 70W A 1102
3AC3SOFTWAREASP A:725 , GLU A:726binding site for residue 70V A 1103
4AC4SOFTWARELEU A:233 , GLU A:849binding site for residue CL A 1104
5AC5SOFTWAREASN A:605 , ASN B:377binding site for residue 70V B 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Arg A:4 -Pro A:5
2Ser A:158 -Pro A:159
3Ser A:199 -Pro A:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5SWP)

(-) 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:1060
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................................eeeeeee.....eeeeeee...hhhhhhhhhhhhhhhh.hhhhh.hhhhheeeee.....eeee...............eeeee......hhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..........hhhhhh.........eeeee......eeee........hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.eeeee.....ee....hhhhhhhhhhhhhhh...eeeeeehhhhhhhh..................hhhhh..eeeeeeeee...........eeeeeeeee........ee..........eeeeeeeeeee.hhh....eeeeeeeee...ee.eeeeee..........eeeeee.ee........................eeeeee..........hhhhhhhhhhhhhhhhh.......hhhhh.........hhhhhhhhhhhh......hhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh....hhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhee.......ee........ee.......eeeeee....hhhhhh.eeeeee.....hhhhhhhhhhhhhhhhhhhhh..........eee.....eeee....eeehhhhhhhh..........hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh........eeee....eee.......hhhhh.............hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5swp A  -26 SYYHHHHHHDYDIPTTFQGAMGSMPPRPSsGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMsELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGWTTK 1054
                                   -17     || -3         7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307||     327       337       347       357       367       377       387       397       407 ||    424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784     | 794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054
                                         -11|            7-SEP                                                                                                                                                                                                                                                                                                      308|                                                                                       409|                                                                                                                                                                                                                                                                                                                                                                                  790-SEP                                                                                                                                                                                                                                                                    
                                           -6                                                                                                                                                                                                                                                                                                                        319                                                                                        417                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhh........ee......eeeeeee..eeeeeee.............hhhhhhhhhh.....................hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5swp B  327 SLQDAEWYSREEVNEKLRDTADGTFLVRTKMHGDYTLTLRKGGNNKLIKIFHRKYGFSDPLTVVELINHYRNESLAQYNPKLDVLLYPVSKQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEEYTRTSQEIQMKRTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIIDSRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKKLNEWL  598
                                   340       350       363       373       383  ||   395 ||    408       418   ||  429||     440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590        
                                 334|                358|                     386|     397|                  422|   430|                                                                                                                                                                      
                                  339                 362                      389      401                   424    432
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5SWP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (109, 132)

Asymmetric/Biological Unit(hide GO term definitions)

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  5swp
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  P85A_HUMAN | P27986
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  PK3CA_HUMAN | P42336
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  2.7.1.153
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  2.7.11.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        P85A_HUMAN | P27986: 1a0n 1azg 1h9o 1pbw 1pht 1pic 1pks 1pkt 2iug 2iuh 2iui 2rd0 2v1y 3hhm 3hiz 3i5r 3i5s 4a55 4jps 4l1b 4l23 4l2y 4ovu 4ovv 4waf 4ykn 4zop 5aul 5fi4 5gji 5itd 5m6u 5sw8 5swg 5swo 5swr 5swt 5sx8 5sx9 5sxa 5sxb 5sxc 5sxd 5sxe 5sxf 5sxi 5sxj 5sxk 5ubt 5uk8 5ukj 5ul1 5vlr
        PK3CA_HUMAN | P42336: 2enq 2rd0 3hhm 3hiz 3zim 4jps 4l1b 4l23 4l2y 4ovu 4ovv 4tuu 4tv3 4waf 4ykn 4zop 5dxh 5dxt 5fi4 5itd 5sw8 5swg 5swo 5swr 5swt 5sx8 5sx9 5sxa 5sxb 5sxc 5sxd 5sxe 5sxf 5sxi 5sxj 5sxk 5ubr 5uk8 5ukj 5ul1

(-) Related Entries Specified in the PDB File

5sw8 5swg 5swo 5swr 5swt 5sx8 5sx9 5sxa 5sxb 5sxc 5sxd 5sxe 5sxf 5sxi 5sxj 5sxk