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(-) Description

Title :  MYO-INOSITOL 3-KINASE BOUND WITH ITS PRODUCTS (ADP AND 1D-MYO-INOSITOL 3-PHOSPHATE)
 
Authors :  R. Nagata, M. Fujihashi, K. Miki
Date :  26 Dec 14  (Deposition) - 03 Jun 15  (Release) - 24 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ribokinase, Product Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Nagata, M. Fujihashi, T. Sato, H. Atomi, K. Miki
Crystal Structure And Product Analysis Of An Archaeal Myo-Inositol Kinase Reveal Substrate Recognition Mode And 3-Oh Phosphorylation
Biochemistry V. 54 3494 2015
PubMed-ID: 25972008  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B00296

(-) Compounds

Molecule 1 - CARBOHYDRATE/PYRIMIDINE KINASE, PFKB FAMILY
    Chains: A, B
    EC Number: 2.7.1.64
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TK2285
    Organism Scientific: THERMOCOCCUS KODAKARAENSIS KOD1
    Organism Taxid: 69014
    Strain: KOD1
    Synonym: MYO-INOSITOL 3-KINASE

 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  (6, 24)

Asymmetric Unit (6, 24)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3INS2Ligand/Ion1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
4IOD15Ligand/IonIODIDE ION
5LIP2Ligand/IonL-MYO-INOSITOL-1-PHOSPHATE
6MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (5, 15)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3INS1Ligand/Ion1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
4IOD11Ligand/IonIODIDE ION
5LIP1Ligand/IonL-MYO-INOSITOL-1-PHOSPHATE
6MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3INS1Ligand/Ion1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
4IOD4Ligand/IonIODIDE ION
5LIP1Ligand/IonL-MYO-INOSITOL-1-PHOSPHATE
6MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:12 , GLY A:25 , GLY A:26 , GLY A:27 , TYR A:30 , TYR A:75 , ARG A:85 , VAL A:112 , GLN A:136 , ARG A:140 , THR A:215 , GLY A:216 , ALA A:217 , GLY A:218 , ASP A:219 , ADP A:302 , INS A:303 , MG A:304 , HOH A:422binding site for residue LIP A 301
02AC2SOFTWAREASN A:83 , HIS A:164 , ASP A:166 , SER A:187 , ASN A:188 , GLY A:189 , PRO A:190 , PHE A:204 , PRO A:206 , VAL A:207 , ALA A:217 , GLY A:218 , THR A:245 , LEU A:249 , LIP A:301 , MG A:304 , HOH A:406 , HOH A:417 , HOH A:422 , HOH A:428 , HOH A:429 , HOH A:431 , HOH A:436binding site for residue ADP A 302
03AC3SOFTWAREASP A:12 , GLY A:25 , GLY A:26 , GLY A:27 , TYR A:30 , TYR A:75 , VAL A:112 , GLN A:136 , ARG A:140 , THR A:215 , ASP A:219 , LIP A:301binding site for residue INS A 303
04AC4SOFTWAREGLN A:136 , LIP A:301 , ADP A:302 , HOH A:414 , HOH A:417 , HOH A:422binding site for residue MG A 304
05AC5SOFTWARETHR A:203 , GLU A:269binding site for residue IOD A 306
06AC6SOFTWAREARG A:92 , IOD A:314binding site for residue IOD A 307
07AC7SOFTWAREARG B:11binding site for residue IOD A 308
08AC8SOFTWARELEU A:99binding site for residue IOD A 312
09AC9SOFTWAREARG A:200 , GLU B:70binding site for residue IOD A 313
10AD1SOFTWAREPRO A:144 , IOD A:307binding site for residue IOD A 314
11AD2SOFTWAREASP A:182 , TYR A:229binding site for residue IOD A 315
12AD3SOFTWARELEU A:80 , ARG A:86 , LYS B:194binding site for residue EDO A 316
13AD4SOFTWAREASP B:12 , GLY B:25 , GLY B:26 , GLY B:27 , TYR B:75 , ARG B:85 , VAL B:112 , GLN B:136 , ARG B:140 , GLY B:216 , ALA B:217 , GLY B:218 , ASP B:219 , ADP B:302 , INS B:303 , MG B:304 , HOH B:414binding site for residue LIP B 301
14AD5SOFTWAREASN B:83 , HIS B:164 , ASP B:166 , SER B:187 , ASN B:188 , GLY B:189 , PRO B:190 , PHE B:204 , PRO B:206 , VAL B:207 , VAL B:209 , VAL B:211 , ALA B:217 , GLY B:218 , THR B:245 , LEU B:249 , LIP B:301 , MG B:304 , HOH B:406 , HOH B:407 , HOH B:410 , HOH B:414 , HOH B:421 , HOH B:422binding site for residue ADP B 302
15AD6SOFTWAREASP B:12 , GLY B:25 , GLY B:26 , GLY B:27 , TYR B:30 , TYR B:75 , LEU B:77 , GLN B:136 , ARG B:140 , THR B:215 , ASP B:219 , LIP B:301binding site for residue INS B 303
16AD7SOFTWAREGLN B:136 , LIP B:301 , ADP B:302 , HOH B:406 , HOH B:410 , HOH B:414binding site for residue MG B 304
17AD8SOFTWARESER B:123binding site for residue IOD B 305
18AD9SOFTWAREARG B:92binding site for residue IOD B 306
19AE1SOFTWAREGLU A:98 , PHE B:228binding site for residue IOD B 307
20AE2SOFTWAREGLU B:201 , ARG B:272 , VAL B:273binding site for residue IOD B 308
21AE3SOFTWAREASP A:101binding site for residues IOD A 305 and IOD A 310

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XF6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp B:101 -Gly B:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XF6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XF6)

(-) Exons   (0, 0)

(no "Exon" information available for 4XF6)

(-) 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:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeeee..eeeeeeehhhhhhhhhhh...eeeeeee....hhhhhhhhhhhheeeee......eeeeee.....eeeeeee..............eeee.......hhhhhhhhhhhh..eeee.hhhh.....ee.....ee.hhhh...eeeeehhhhh.ee..hhhhh.eeeee.....eeeee..eeeeee..........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xf6 A   1 MKCLVVGHVVRDIVKKGNKVLERLGGGAYYSALALSRFCDVEILTSFSNLPEEWIKELESMAKLQVVPSETTTTYELTYLDGNRRRLKLLERASPIEELPDGEYDVLLMNPVAREVPPALVTSALKKFPFVAVDIQGFIRSSSPGEIQYQPIDGSFLKGVKILHADLGEYQYLQGFSPEFVDVLLLSNGPEPGKAFLHGREYTFEPVHVGVDESTGAGDVFLGAFTGFYSQCPFVQALKRAAAFTALFLKNRSVDFSMDDVNELAMKVEVKRV 273
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   


Chain B from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeeee..eeeeeeehhhhhhhhhhh...eeeeeee....hhhhhhhhhhhheeeee......eeeeee.....eeeeeee..............eeee.......hhhhhhhhhhhh..eeee.hhhh.....ee.....ee.hhhh...eeeeehhhhh.ee..hhhhh.eeeee.....eeeee..eeeeee..........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xf6 B   1 MKCLVVGHVVRDIVKKGNKVLERLGGGAYYSALALSRFCDVEILTSFSNLPEEWIKELESMAKLQVVPSETTTTYELTYLDGNRRRLKLLERASPIEELPDGEYDVLLMNPVAREVPPALVTSALKKFPFVAVDIQGFIRSSSPGEIQYQPIDGSFLKGVKILHADLGEYQYLQGFSPEFVDVLLLSNGPEPGKAFLHGREYTFEPVHVGVDESTGAGDVFLGAFTGFYSQCPFVQALKRAAAFTALFLKNRSVDFSMDDVNELAMKVEVKRV 273
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
   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 4XF6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XF6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XF6)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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4xf7