Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF PI3KDELTA WITH COMPOUND 32
 
Authors :  J. R. Somoza, A. G. Villasenor
Date :  16 Feb 16  (Deposition) - 22 Feb 17  (Release) - 22 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.84
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Keywords :  Kinase, P110, Kinase Inhibitor, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Somoza, A. G. Villasenor
The Crystal Structure Of Pi3Kdelta With Compound 32
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT DELTA ISOFORM
    Chains: A
    EC Number: 2.7.1.153
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 106-1043
    Gene: PIK3CD
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: PTDINS-3-KINASE SUBUNIT DELTA,PHOSPHATIDYLINOSITOL 4,5- BISPHOSPHATE 3-KINASE 110 KDA CATALYTIC SUBUNIT DELTA,P110DELTA

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
168R1Ligand/Ion2-[(1S)-1-({6-AMINO-5-[(1H-PYRAZOL-4-YL)ETHYNYL]PYRIMIDIN-4-YL}AMINO)ETHYL]-5-CHLORO-3-PHENYLQUINAZOLIN-4(3H)-ONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
168R1Ligand/Ion2-[(1S)-1-({6-AMINO-5-[(1H-PYRAZOL-4-YL)ETHYNYL]PYRIMIDIN-4-YL}AMINO)ETHYL]-5-CHLORO-3-PHENYLQUINAZOLIN-4(3H)-ONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:750 , PHE A:751 , MET A:752 , PRO A:758 , LEU A:759 , TRP A:760 , ILE A:777 , LYS A:779 , ASP A:787 , ILE A:825 , GLU A:826 , VAL A:827 , VAL A:828 , SER A:831 , ASP A:832 , MET A:900 , ILE A:910 , ASP A:911binding site for residue 68R A 1101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I6U)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:367 -Glu A:368
2Thr A:434 -Gly A:435

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I6U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I6U)

(-) Exons   (0, 0)

(no "Exon" information available for 5I6U)

(-) 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:816
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh........eee.ee...........eee...hhhhhhhhhhhh.......hhh.eeeee.....ee..........hhhhhh......eeeeeehhhhhhhhhhh........eeeeeeeee...eeeeeeeee..............ee.........eeeeeee........eeeeeee.......eeeeee..........eeeeee.ee....................eeeeee.............................hhhhhhhhhhhhhhhh..hhhhhhh.....hhhhhhhhhhhhh.....hhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee..eeeeee.ee.hhhhee.......eeeeeehhhhhhhhh.eeeeee...hhhhhhhhhhhhhhhhhhhh...........eeeee..eeeee....eeehhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhh.eeee....eee................hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5i6u A  109 VKKLINSQISLLIGKGLHEFDSLRDPEVNDFRTKMRQFCEEAAAHRQQLGWVEWLQYSFPLQLEPNRALLVNVKFEGSEESFTFQVSTKDMPLALMACALRKKATVFRQQPEEYALQVNGRHEYLYGNYPLCHFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSNLWSLEQPFSIELIEGRKMKLVVQAGLFHGNEMLCKTVSSSEVNVCSEPVWKQRLEFDISVCDLPRMARLCFALYAVVDCPIAWANLMLFDYKDQLKTGERCLYMWPSVLLNPAGTVRGNPNTESAAALVIYLPEVAPVYFPALEKILELLREILERELYEHEKDLVWKMRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCYVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLGRALANRKIGHFLFWHLRSEMHVPSVALRFGLIMEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKVSSQKTTKPQTKEMMHMCMRQETYMEALSHLQSPLDPSTLLEEVCVEQCTFMDSKMKPLWIMYSSEEAGSAGNVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLHSDTIANIQLNKSNMAAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFLGNFRVPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEALRES 1026
                                   118       128       138       148       158       168    || 191       201       211       221       235       245       255       265       275       285     ||319       329  ||   345       355       365       375       385       395  ||   421       431       441   ||  457       467       477 ||    489    || 515 ||    529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839     ||851       861       871       881       891       901       911       930       940       950       960       970       980       990      1000      1010      1020      
                                                                                          173|                                        230|                                                     291|             332|                                                        398|                           445|                        479|         494|   517|                                                                                                                                                                                                                                                                                                                                845|                                                                    919|                                                                                                 
                                                                                           187                                         235                                                      316              339                                                         415                            452                         482          511    522                                                                                                                                                                                                                                                                                                                                 848                                                                     929
   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 5I6U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I6U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I6U)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    68R  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:367 - Glu A:368   [ RasMol ]  
    Thr A:434 - Gly A:435   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5i6u
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PK3CD_MOUSE | O35904
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.1.153
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PK3CD_MOUSE | O35904
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PK3CD_MOUSE | O35904: 2wxf 2wxg 2wxh 2wxi 2wxj 2wxk 2wxl 2wxm 2wxn 2wxo 2wxp 2wxq 2wxr 2x38 4ajw 4v0i 4xe0 5ae8 5ae9 5i4u 5is5 5l72 5ncy 5ncz 5t27 5t28 5t2b 5t2d 5t2g 5t2i 5t2l 5t2m 5t7f 5t8i

(-) Related Entries Specified in the PDB File

5i4u