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(-) Description

Title :  CRYSTAL STRUCTURE OF INPP5B IN COMPLEX WITH BIPHENYL 3,3',4, 4',5,5'-HEXAKISPHOSPHATE
 
Authors :  L. Tresaugues, S. J. Mills, C. Silvander, G. Cozier, B. V. L. Potter, P.
Date :  06 Jul 15  (Deposition) - 13 Apr 16  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.89
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Sgc, Signalling, Structural Genomics Consortium Stockholm, Magnesium Binding, Protein-Inhbitor Complex, Inhibitor, Phosphoinositides Signalling (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Mills, C. Silvander, G. Cozier, L. Tresaugues, P. Nordlund, B. V. L. Potter
Crystal Structures Of Type-Ii Inositol Polyphosphate 5- Phosphatase Inpp5B With Synthetic Inositol Polyphosphate Surrogates Reveal New Mechanistic Insights For The Inositol 5-Phosphatase Family.
Biochemistry V. 55 1384 2016
PubMed-ID: 26854536  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B00838

(-) Compounds

Molecule 1 - TYPE II INOSITOL 1,4,5-TRISPHOSPHATE 5-PHOSPHATASE
    Chains: A
    EC Number: 3.1.3.36
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-CH2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: R3 PRARE
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 339-643
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CLONED WITH A C-TERMINAL HEXAHISTIDINE TAG
    Other Details - Source: MAMMALIAN GENE COLLECTION (MGC)
    Synonym: 75 KDA INOSITOL POLYPHOSPHATE-5-PHOSPHATASE, PHOSPHOINOSITIDE 5-PHOSPHATASE, 5PTASE, TYPE II INOSITOL 1,4,5- TRISPHOSPHATE 5-PHOSPHATASE, ISOFORM 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
1B6K1Ligand/IonBIPHENYL 3,3',4,4',5,5'-HEXAKISPHOSPHATE
2CL1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4MG1Ligand/IonMAGNESIUM ION
5PO43Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:373 , MET A:374 , ARG A:410 , HIS A:567BINDING SITE FOR RESIDUE GOL A1571
2AC2SOFTWAREMET A:258 , GLU A:303 , ASN A:379 , LYS A:380 , HIS A:400 , ALA A:403 , HIS A:404 , TYR A:502 , LYS A:516 , ARG A:518 , HIS A:565 , HIS A:566 , HIS A:567 , HIS A:568 , HIS A:569 , HIS A:570 , PO4 A:1573 , MG A:1574 , HOH A:2027BINDING SITE FOR RESIDUE B6K A1572
3AC3SOFTWAREASN A:273 , GLU A:303 , HIS A:400 , ASP A:447 , ASN A:449 , ARG A:451 , HIS A:549 , B6K A:1572 , MG A:1574BINDING SITE FOR RESIDUE PO4 A1573
4AC4SOFTWAREASN A:275 , GLU A:303 , ASP A:548 , B6K A:1572 , PO4 A:1573BINDING SITE FOR RESIDUE MG A1574
5AC5SOFTWARETYR A:473 , LYS A:479 , VAL A:482 , GLU A:493 , HOH A:2021BINDING SITE FOR RESIDUE PO4 A1575
6AC6SOFTWAREGLY A:370 , ARG A:376 , ARG A:421BINDING SITE FOR RESIDUE PO4 A1576
7AC7SOFTWARELYS A:338 , LEU A:341BINDING SITE FOR RESIDUE CL A1577

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A7I)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:502 -Lys A:503

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A7I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A7I)

(-) Exons   (0, 0)

(no "Exon" information available for 5A7I)

(-) 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:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee.........hhhhhh.......eeeeeee....hhhhhh....hhhhhhhhhhhhhh.....eeeeeeeee..eeeeeeee.hhhh.eeeeeeeeee.hhhhh....eeeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhhhhhh..................eeeeeee........hhhhhhhhhhh.hhhhhhh.hhhhhhhhh.......................................eeeeeee..eeeeeeee...........eeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a7i A 258 MYTYIQNFRFFAGTYNVNGQSPKECLRLWLSNGIQAPDVYCVGFQELDLSKEAFFFHDTPKEEEWFKAVSEGLHPDAKYAKVKLIRLVGIMLLLYVKQEHAAYISEVEAETVGTGIMGRMGNKGGVAIRFQFHNTSICVVNSHLAAHIEEYERRNQDYKDICSRMQFCQPDPSLPPLTISNHDVILWLGDLNYRIEELDVEKVKKLIEEKDFQMLYAYDQLKIQVAAKTVFEGFTEGELTFQPTYKYDTGSDDWDTSEKCRAPAWCDRILWKGKNITQLSYQSHMALKTSDHKPVSSVFDIGVRVVAHHHHHH 570
                                   267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567
   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 5A7I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A7I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A7I)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Tyr A:502 - Lys A:503   [ RasMol ]  
 

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 Related Entries

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        I5P2_HUMAN | P32019: 3mtc 3n9v 4cml 5a7j

(-) Related Entries Specified in the PDB File

5a7j CRYSTAL STRUCTURE OF INPP5B IN COMPLEX WITH BENZENE 1 ,2,4,5-TETRAKISPHOSPHATE