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

(-) Description

Title :  PI4KB IN COMPLEX WITH RAB11 AND THE MI359 INHIBITOR
 
Authors :  D. Chalupska, I. Mejdrova, R. Nencka, E. Boura
Date :  14 Dec 15  (Deposition) - 28 Dec 16  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.28
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Inhibitor, Complex, Kinase, Lipid, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Chalupska, I. Mejdrova, R. Nencka, E. Boura
Pi4Kb In Complex With Rab11 And The Mi359 Inhibitor
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 4-KINASE BETA,PHOSPHATIDYLINOSITOL 4- KINASE BETA
    ChainsA
    EC Number2.7.1.67, 2.7.1.67
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 128-422, 523-799
    GenePI4KB, PIK4CB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPTDINS 4-KINASE BETA,NPIK,PI4K92,PI4KB,PTDINS 4-KINASE BETA, NPIK,PI4K92,PI4KB
 
Molecule 2 - RAS-RELATED PROTEIN RAB-11A
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneRAB11A, RAB11
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRAB-11,YL8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
15W71Ligand/Ion~{N}-[2-[[3-[3-[(4-AZANYLCYCLOHEXYL)SULFAMOYL]-4-METHOXY-PHENYL]-6-CHLORANYL-2-METHYL-IMIDAZO[1,2-B]PYRIDAZIN-8-YL]AMINO]ETHYL]ETHANAMIDE
2GSP1Ligand/Ion5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:374 , PRO A:381 , ILE A:562 , LYS A:564 , TYR A:598 , ILE A:610 , GLU A:611 , PRO A:612 , VAL A:613 , VAL A:614 , ALA A:616 , GLY A:675 , LEU A:678 , ILE A:688 , ASP A:689binding site for residue 5W7 A 801
2AC2SOFTWARESER B:20 , GLY B:21 , VAL B:22 , GLY B:23 , LYS B:24 , SER B:25 , ASN B:26 , ASN B:37 , LEU B:38 , SER B:40 , SER B:42 , THR B:43 , GLY B:69 , ASN B:124 , LYS B:125 , ASP B:127 , LEU B:128 , SER B:154 , ALA B:155 , LEU B:156binding site for residue GSP B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FBR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FBR)

(-) 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:465
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.............eeeee.hhhhhee........eeeeeeeee..hhhhh..............hhhhhhhhhhhhh.......eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh..........eee.....eee.....eeehhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.........eeee....eee.............hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fbr A 128 SWLLRLFESKLFDISMAISYLYNSKEPGVQAYIGNRLFCFRNEDVDFYLPQLLNMYIHMDEDVGDAIKPYIVHRCRQSINFSLQCALLLGAYSSRGTKLRKLILSRLAPEREFIKSLMAIGKRLATLPTKEQKTQRLISELSLLNHKLPARVWLPTAGFDHHVVRVPHTQAVVLNSKDKAPYLIYVEVLECENFDTTSVPARIPENVALKEPWQEKVRRIREGSPYGHLPNWRLLSVIVKCGDDLRQELLAFQVLKQLQSIWEQERVPLWIKPYKILVISADSGMIEPVVNAVSIHQVKKQSQLSLLDYFLQEHGSYTTEAFLSAQRNFVQSCAGYCLVCYLLQVKDRHNGNILLDAEGHIIHIDFGFILSSSFKLTTEFVDVMGGLDGDMFNYYKMLMLQGLIAARKHMDKVVQIVEIMQQGSQLPCFHGSSTIRNLKERFHMSMTEEQLQLLVEQMVDGSMRS 799
                                   137       147       157       167       177       187       197       207       217   ||  237    || 310       320       330       340       350       360       370       380       390       400     ||534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694  ||   714       724       734       744       754       764       774       784       794     
                                                                                                                       221|       242|                                                                                                 406|                                                                                                                                                                   697|                                                                                           
                                                                                                                        232        306                                                                                                  531                                                                                                                                                                    708                                                                                           

Chain B from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee....hhhhhhhhhhhh............eeeee..ee..ee..eeeee......hhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhh..hhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fbr B   8 YDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKAQIWDTAGRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVSQ 178
                                    17        27        37        47        57        67 ||     81        91       101       111       121       131       141       151       161       171       
                                                                                        69|                                                                                                        
                                                                                         74                                                                                                        

   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 5FBR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (73, 82)

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
    5W7  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GSP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5fbr)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5fbr
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PI4KB_HUMAN | Q9UBF8
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  RB11A_HUMAN | P62491
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.1.67
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PI4KB_HUMAN | Q9UBF8
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  RB11A_HUMAN | P62491
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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