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(-) Description

Title :  CRYSTAL STRUCTURE OF THE P-REX1 PH DOMAIN WITH INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE BOUND
 
Authors :  J. N. Cash, J. J. G. Tesmer
Date :  06 Aug 15  (Deposition) - 20 Apr 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pleckstrin Homology Domain, Beta Sandwich, Phosphatidylinositol- Binding, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. N. Cash, E. M. Davis, J. J. Tesmer
Structural And Biochemical Characterization Of The Catalyti Core Of The Metastatic Factor P-Rex1 And Its Regulation By Ptdins(3, 4, 5)P3.
Structure V. 24 730 2016
PubMed-ID: 27150042  |  Reference-DOI: 10.1016/J.STR.2016.02.022

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 3,4,5-TRISPHOSPHATE-DEPENDENT RAC EXCHANGER 1 PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMALC2H10T
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 245-408
    GenePREX1, KIAA1415
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPTDINS(3,4,5)-DEPENDENT RAC EXCHANGER 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
14IP2Ligand/IonINOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
14IP1Ligand/IonINOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
14IP1Ligand/IonINOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:280 , SER A:282 , ASN A:285 , GLN A:287 , ARG A:289 , TYR A:300 , ARG A:328 , LYS A:366 , LYS A:368 , ARG A:389 , HOH A:602 , HOH A:634 , HOH A:642 , HOH A:643 , HOH A:676 , HOH A:684 , GLN B:287 , ARG B:289 , LYS B:302 , 4IP B:501 , HOH B:695binding site for residue 4IP A 501
2AC2SOFTWAREGLN A:287 , ARG A:289 , LYS A:302 , 4IP A:501 , LYS B:280 , SER B:282 , ASN B:285 , GLN B:287 , ARG B:289 , TYR B:300 , ARG B:328 , LYS B:366 , LYS B:368 , HOH B:602 , HOH B:616 , HOH B:620 , HOH B:623 , HOH B:639 , HOH B:681binding site for residue 4IP B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D3Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D3Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D3Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D3Y)

(-) Exons   (0, 0)

(no "Exon" information available for 5D3Y)

(-) 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:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhee.....hhhhhh..eeeeeeeeeee..eeeeeeeeee..eeeeeee......eeeeeeee.hhheeee.................eeeeeehhhheeeeee..hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d3y A 249 ALEQLQSHIEGWEGSNLTDICTQLLLQGTLLKISAGNIQERAFFLFDNLLVYCKRKSRVSLYIFRGRINTEVMEVENVEDGTADYHSNGYTVTNGWKIHNTAKNKWFVCMAKTAEEKQKWLDAIIREREQRESLKL 399
                                   258       268       278       288       298       323       333       343       353       363       373       383       393      
                                                                                    307|                                                                            
                                                                                     323                                                                            

Chain B from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhee.....hhhhhh..eeeeeeeeeee..eeeeeeeeee..eeeeeee......eeeeeeee.hhheeee.................eeeeeehhhheeeeee..hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d3y B 249 ALEQLQSHIEGWEGSNLTDICTQLLLQGTLLKISAGNIQERAFFLFDNLLVYCKRKSRVSLYIFRGRINTEVMEVENVEDGTADYHSNGYTVTNGWKIHNTAKNKWFVCMAKTAEEKQKWLDAIIREREQRESLKL 399
                                   258       268       278       288       298       323       333       343       353       363       373       383       393      
                                                                                    307|                                                                            
                                                                                     323                                                                            

   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 5D3Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D3Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D3Y)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PREX1_HUMAN | Q8TCU63qik 4yon 5d27 5d3v 5d3w 5d3x 5fi0 5fi1

(-) Related Entries Specified in the PDB File

5d27 5D27 CONTAINS THE SAME PROTEIN WITH NO LIGAND BOUND.
5d3z