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(-) Description

Title :  CRYSTAL STRUCTURE OF INPP5B IN COMPLEX WITH BENZENE 1,2,4,5-TETRAKISPHOSPHATE
 
Authors :  L. Tresaugues, S. J. Mills, C. Silvander, G. Cozier, B. V. L. Potter, P. N
Date :  06 Jul 15  (Deposition) - 13 Apr 16  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
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, B
    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

  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  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2K2Y2Ligand/IonBENZENE 1,2,4,5-TETRAYL TETRAKIS[DIHYDROGEN (PHOSPHATE)
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2K2Y1Ligand/IonBENZENE 1,2,4,5-TETRAYL TETRAKIS[DIHYDROGEN (PHOSPHATE)
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2K2Y1Ligand/IonBENZENE 1,2,4,5-TETRAYL TETRAKIS[DIHYDROGEN (PHOSPHATE)
3SO43Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:473 , VAL B:482 , GLU B:493BINDING SITE FOR RESIDUE GOL B1567
2AC2SOFTWAREHIS B:566BINDING SITE FOR RESIDUE SO4 B1568
3AC3SOFTWAREILE B:373 , MET B:374 , ARG B:410BINDING SITE FOR RESIDUE SO4 B1569
4AC4SOFTWARELYS A:531 , ASN A:532 , ARG A:561BINDING SITE FOR RESIDUE SO4 A1567
5AC5SOFTWAREMET B:258 , HIS B:565 , HIS B:566 , HOH B:2037BINDING SITE FOR RESIDUE K2Y B1570
6AC6SOFTWAREMET A:258 , HIS A:565 , HIS A:566 , HOH A:2035 , HOH A:2036BINDING SITE FOR RESIDUE K2Y A1568
7AC7SOFTWARELYS B:531 , ASN B:532 , ARG B:561BINDING SITE FOR RESIDUE SO4 B1571

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A7J)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:502 -Lys A:503
2Tyr B:502 -Lys B:503

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A7J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A7J)

(-) Exons   (0, 0)

(no "Exon" information available for 5A7J)

(-) 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:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee.........hhhhhh.......eeeeeee....hhhhhh...hhhhhhhhhhhhhhh.....eeeeeeeee..eeeeeeee.hhhh.eeeeeeeeee.hhhhh....eeeeeeeee..eeeeeeeee......hhhhhhhhhhhhhhhhee.........ee.....eeeeeee........hhhhhhhhhhh.hhhhhhh.hhhhhhhhh.......ee.................................eeee..eeeeeeee...........eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a7j A 258 MYTYIQNFRFFAGTYNVNGQSPKECLRLWLSNGIQAPDVYCVGFQELDLSKEAFFFHDTPKEEEWFKAVSEGLHPDAKYAKVKLIRLVGIMLLLYVKQEHAAYISEVEAETVGTGIMGRMGNKGGVAIRFQFHNTSICVVNSHLAAHIEEYERRNQDYKDICSRMQFCQPDPSLPPLTISNHDVILWLGDLNYRIEELDVEKVKKLIEEKDFQMLYAYDQLKIQVAAKTVFEGFTEGELTFQPTYKYDTGSDDWDTSEKCRAPAWCDRILWKGKNITQLSYQSHMALKTSDHKPVSSVFDIGVRVVAHH 566
                                   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         


Chain B from PDB  Type:PROTEIN  Length:309
                                                                                                                                                                                                                                                                                                                                                     
               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......hhhhhhhhhhhhhhhhee.........ee.....eeeeeee........hhhhhhhhhhh.hhhhhhh.hhhhhhhhh.......ee.................................eeee..eeeeeeee...........eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a7j B 258 MYTYIQNFRFFAGTYNVNGQSPKECLRLWLSNGIQAPDVYCVGFQELDLSKEAFFFHDTPKEEEWFKAVSEGLHPDAKYAKVKLIRLVGIMLLLYVKQEHAAYISEVEAETVGTGIMGRMGNKGGVAIRFQFHNTSICVVNSHLAAHIEEYERRNQDYKDICSRMQFCQPDPSLPPLTISNHDVILWLGDLNYRIEELDVEKVKKLIEEKDFQMLYAYDQLKIQVAAKTVFEGFTEGELTFQPTYKYDTGSDDWDTSEKCRAPAWCDRILWKGKNITQLSYQSHMALKTSDHKPVSSVFDIGVRVVAHH 566
                                   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
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  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 5A7J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A7J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A7J)

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)

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        I5P2_HUMAN | P32019: 3mtc 3n9v 4cml 5a7i

(-) Related Entries Specified in the PDB File

5a7i CRYSTAL STRUCTURE OF INPP5B IN COMPLEX WITH BIPHENYL 3 ,3',4,4',5,5'-HEXAKISPHOSPHATE