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

(-) Description

Title :  CRYSTAL STRUCTURE OF PIP4KIIBETA
 
Authors :  K. Takeuchi, Y. H. Lo, K. Sumita, M. Senda, J. Terakawa, A. Dimitoris, J. W. Locasale, M. Sasaki, H. Yoshino, Y. Zhang, E. R. Kahoud, T. Takano T. Yokota, B. Emerling, J. A. Asara, T. Ishida, I. Shimada, T. Daikoku, L. C. Cantley, T. Senda, A. T. Sasaki
Date :  08 Oct 14  (Deposition) - 14 Oct 15  (Release) - 03 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lipid Kinase, Phosphoinositide Signaling, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Sumita, Y. H. Lo, K. Takeuchi, M. Senda, S. Kofuji, Y. Ikeda, J. Terakawa, M. Sasaki, H. Yoshino, N. Majd, Y. Zheng, E. R. Kahoud, T. Yokota, B. M. Emerling, J. M. Asara, T. Ishida, J. W. Locasale, T. Daikoku, D. Anastasiou, T. Senda, A. T. Sasaki
The Lipid Kinase Pi5P4K Beta Is An Intracellular Gtp Sensor For Metabolism And Tumorigenesis
Mol. Cell V. 61 187 2016
PubMed-ID: 26774281  |  Reference-DOI: 10.1016/J.MOLCEL.2015.12.011

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 5-PHOSPHATE 4-KINASE TYPE-2 BETA
    Chains: A, B
    EC Number: 2.7.1.149
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 31-416
    Gene: PIP4K2B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 1-PHOSPHATIDYLINOSITOL 5-PHOSPHATE 4-KINASE 2-BETA, DIPHOSPHOINOSITIDE KINASE 2-BETA, PHOSPHATIDYLINOSITOL 5-PHOSPHATE 4- KINASE TYPE II BETA, PI(5)P 4-KINASE TYPE II BETA, PIP4KII-BETA, PTDINS(5)P-4-KINASE ISOFORM 2-BETA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3WZZ)

(-) Sites  (0, 0)

(no "Site" information available for 3WZZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WZZ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:137 -Arg A:138
2Phe B:336 -Phe B:337

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WZZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WZZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3WZZ)

(-) 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:322
                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhh........hhhhhh.eeeeeeeee.........eeeeeeehhhhhhhhhhhh..hhhhhhhhhhh...ee...eee.....eeeeeehhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeeee..........eeeee.........hhhhhhh...eehhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhhhhhhhhhh............eee........eeeeeeee......hhhhhhhhhhhhhhhhee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wzz A  32 KVKLFRASEPILSVLMWGVNHTINELSNVPVPVMLMPDDFKAYSKIKVDNHLFNKENLPSRFKFKEYCPMVFRNLRERFGIDDQDYQNSVTRSAPINSTRFLTTYDRRFVIKTVSSEDVAEMHNILKKYHQFIVECHGNTLLPQFLGMYRLTVDGVETYMVVTRNVFSHRLTVHRKYDLKGSTVAREASDKEKAKDLPTFKDNDFLNEGQKLHVGEESKKNFLEKLKRDVEFLAQLKIMDYSLLVGIHDVDRAEQEEMEVEERAEDEGPGEFDPSVDVYAMKSHESSPKKEVYFMAIIDILTTVNPEQYSKRFNEFMSNILT 416
                                    41        51        61        71        81        91       101       111       121       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298      |340       350       360       370 ||    404       414  
                                                                                                                           129|                                                                                                                                                                     305|                               372|                   
                                                                                                                            137                                                                                                                                                                      338                                397                   


Chain B from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhh.......hhhhhh.eeeeeee...........eeeeeeehhhhhhhhhhhh..hhhhhhhhhhh......eee.....eeeeeehhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeeee..........eeeee........hhhhhh....eeehhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeehhhhh...............eee........eeeeeeee......hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wzz B  32 KVKLFRASEPILSVLMWGVNHTINELSNVPVPVMLMPDDFKAYSKIKVDNHLFNKENLPSRFKFKEYCPMVFRNLRERFGIDDQDYQNSVTRSAPINRFLTTYDRRFVIKTVSSEDVAEMHNILKKYHQFIVECHGNTLLPQFLGMYRLTVDGVETYMVVTRNVFSHRLTVHRKYDLKGSVAREASDKEKAKDLPTFKDNDFLNELHVGEESKKNFLEKLKRDVEFLAQLKIMDYSLLVGIHDVDRAEQFFGPGEFDPSVDVYAMKSHESSPKKEVYFMAIIDILTTVNPEQYSKRFNEFMSNILT 416
                                    41        51        61        71        81        91       101       111       121      |140       150       160       170       180       190       200       210       220|      231       241    || 254       264       274       284       336       346       356       366     ||400       410      
                                                                                                                          128|                                                                               220|                     246|                                        293|                                 372|                   
                                                                                                                           138                                                                                222                      250                                         336                                  397
   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 3WZZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WZZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WZZ)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
(no "Ligands, Modified Residues, Ions" information available for 3wzz)
 
  Sites
(no "Sites" information available for 3wzz)
 
  Cis Peptide Bonds
    Phe B:336 - Phe B:337   [ RasMol ]  
    Thr A:137 - Arg A:138   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit 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
  3wzz
    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
  PI42B_HUMAN | P78356
    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)
  2.7.1.149
    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
  PI42B_HUMAN | P78356
    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
        PI42B_HUMAN | P78356: 1bo1 3x01 3x02 3x03 3x04 3x05 3x06 3x07 3x08 3x09 3x0a 3x0b 3x0c

(-) Related Entries Specified in the PDB File

3x01 3x02 3x03 3x04 3x05 3x06 3x07 3x08 3x09 3x0a 3x0b 3x0c