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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN DIPHOSPHOINOSITOL PENTAKISPHOSPHATE KINASE 2 (PPIP5K2) IN COMPLEX WITH AMPPNP AND A SUBSTRATE ANALOG 5PA-IP5
 
Authors :  H. Wang
Date :  18 Oct 12  (Deposition) - 31 Oct 12  (Release) - 07 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Atp-Grasp Fold, Inositol Pyrophosphate Kinase, Phosphoryl Transferase, Pyrophosphate Analog, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Riley, H. Wang, J. D. Weaver, S. B. Shears, B. V. Potter
First Synthetic Analogues Of Diphosphoinositol Polyphosphates: Interaction With Pp-Insp(5) Kinase.
Chem. Commun. (Camb. ) V. 48 11292 2012
PubMed-ID: 23032903  |  Reference-DOI: 10.1039/C2CC36044F

(-) Compounds

Molecule 1 - INOSITOL HEXAKISPHOSPHATE AND DIPHOSPHOINOSITOL- PENTAKISPHOSPHATE KINASE 2
    Chains: A
    EC Number: 2.7.4.21, 2.7.4.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST566
    Expression System Strain: ARCTIC EXPRESS (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ATP-GRASP KINASE DOMAIN
    Gene: HISPPD1, KIAA0433, PPIP5K2, VIP2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DIPHOSPHOINOSITOL PENTAKISPHOSPHATE KINASE 2, HISTIDINE ACID PHOSPHATASE DOMAIN-CONTAINING PROTEIN 1, INSP6 AND PP-IP5 KINASE 2, VIP1 HOMOLOG 2, HSVIP2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
10EJ1Ligand/Ion(2-OXO-2-{[(1S,2R,3S,4S,5R,6S)-2,3,4,5,6-PENTAKIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}ETHYL)PHOSPHONICACID
2ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3MG4Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:134 , PRO A:149 , LYS A:187 , HIS A:194 , LEU A:211 , ARG A:213 , GLU A:237 , GLU A:238 , PHE A:239 , MET A:240 , ASP A:246 , LYS A:248 , ARG A:262 , SER A:264 , ASP A:309 , LEU A:311 , CYS A:320 , ASP A:321 , ASN A:323 , 0EJ A:402 , MG A:403 , MG A:404 , HOH A:571 , HOH A:579 , HOH A:737 , HOH A:738 , HOH A:778BINDING SITE FOR RESIDUE ANP A 401
2AC2SOFTWARELYS A:53 , LYS A:54 , ARG A:213 , LYS A:214 , LYS A:248 , ARG A:281 , SER A:326 , LYS A:329 , ANP A:401 , HOH A:557 , HOH A:573 , HOH A:575 , HOH A:592 , HOH A:593 , HOH A:613 , HOH A:648 , HOH A:653 , HOH A:712 , HOH A:729 , HOH A:737 , HOH A:830BINDING SITE FOR RESIDUE 0EJ A 402
3AC3SOFTWAREASP A:321 , ASN A:323 , ANP A:401 , HOH A:738BINDING SITE FOR RESIDUE MG A 403
4AC4SOFTWAREASP A:309 , ASP A:321 , ANP A:401BINDING SITE FOR RESIDUE MG A 404
5AC5SOFTWARESER A:68 , PHE A:70 , ILE A:73 , HOH A:657 , HOH A:695 , HOH A:777BINDING SITE FOR RESIDUE MG A 405
6AC6SOFTWAREHOH A:560 , HOH A:573 , HOH A:628 , HOH A:653 , HOH A:686 , HOH A:776BINDING SITE FOR RESIDUE MG A 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HN2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:182 -Pro A:183

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HN2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HN2)

(-) Exons   (0, 0)

(no "Exon" information available for 4HN2)

(-) 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:325
                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhh....eeee......hhhhhhhhhhhhh.ee....hhhhhh.hhhhhhhhhhhh......eeee...........eee...eeee..eeee..eeeee........eee.hhhhh..eeeeeeee..eeeeee..........eeeee......eeeeeeee....eeeeeee..................ee...hhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeee......hhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hn2 A  42 RQIVVGICSMAKKSKSKPMKEILERISLFKYITVVVFEEEVILNEPVENWPLCDCLISFHSKGFPLDKAVAYAKLRNPFVINDLNMQYLIQDRREVYSILQAEGILLPRYAILNRDPNNPKECNLIEGEDHVEVNGEVFQKPFVEKPVSAEDHNVYIYYPTSAGGGSQRLFRKIGSRSSVYSPESNVRKTGSYIYEEFMPTDGTDVKVYTVGPDYAHAEARKSPALDGKVERDSEGKEVRYPVILNAREKLIAWKVCLAFKQTVCGFDLLRANGQSYVCDVNGFSFVKNSMKYYDDCAKILGNIVMRELAPQFHIPWSIPLEAED 366
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361
   Legend:   → Mismatch (orange background)
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    → 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 4HN2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HN2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HN2)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Lys A:182 - Pro A:183   [ RasMol ]  
 

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  4hn2
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  VIP2_HUMAN | O43314
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  2.7.4.21
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  2.7.4.24
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 Related Entries

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

UniProtKB/Swiss-Prot
        VIP2_HUMAN | O43314: 3t54 3t7a 3t99 3t9a 3t9b 3t9c 3t9d 3t9e 3t9f 4nzm 4nzn 4nzo 4q4c 4q4d 5bya 5byb 5dgh 5dgi

(-) Related Entries Specified in the PDB File

3t9b CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN DIPHOSPHOINOSITOL PENTAKISPHOSPHATE KINASE 2 (PPIP5K2) IN COMPLEX WITH AMPPNP AT PH 5.2
3t9d CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN DIPHOSPHOINOSITOL PENTAKISPHOSPHATE KINASE 2 (PPIP5K2) IN COMPLEX WITH AMPPNP AND 5-(PP)-IP5 (5-IP7)