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(-) Description

Title :  MYO-INOSITOL 3-KINASE BOUND WITH ITS SUBSTRATES (AMPPCP AND MYO-INOSITOL)
 
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 :  1.93
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ribokinase, Substrate 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  (4, 28)

Asymmetric Unit (4, 28)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2INS2Ligand/Ion1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
3IOD22Ligand/IonIODIDE ION
4MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
1ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2INS1Ligand/Ion1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
3IOD12Ligand/IonIODIDE ION
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2INS1Ligand/Ion1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
3IOD10Ligand/IonIODIDE ION
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:12 , GLY A:25 , GLY A:26 , GLY A:27 , TYR A:30 , TYR A:75 , GLN A:136 , ARG A:140 , THR A:215 , ASP A:219 , HOH A:448 , HOH A:456binding site for residue INS A 301
02AC2SOFTWAREASN A:83 , ARG A:85 , 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 , VAL A:209 , SER A:214 , GLY A:216 , ALA A:217 , GLY A:218 , THR A:245 , LEU A:249 , MG A:303 , HOH A:426 , HOH A:428 , HOH A:430 , HOH A:435 , HOH A:447 , HOH A:448 , HOH A:456binding site for residue ACP A 302
03AC3SOFTWAREGLN A:136 , ACP A:302 , HOH A:426 , HOH A:435 , HOH A:447 , HOH A:448binding site for residue MG A 303
04AC4SOFTWAREGLU A:59 , LEU A:64 , HOH A:411binding site for residue IOD A 304
05AC5SOFTWARETHR A:203 , GLU A:269binding site for residue IOD A 305
06AC6SOFTWAREASP A:101 , IOD A:309 , GLN B:236 , IOD B:310binding site for residue IOD A 308
07AC7SOFTWAREIOD A:308 , IOD B:310binding site for residue IOD A 309
08AC8SOFTWAREGLU B:146binding site for residue IOD A 310
09AC9SOFTWARELEU A:99binding site for residue IOD A 311
10AD1SOFTWARELEU A:99 , SER A:123 , ALA A:124 , LYS A:127binding site for residue IOD A 312
11AD2SOFTWAREARG A:85 , ILE A:147binding site for residue IOD A 313
12AD3SOFTWAREVAL A:235binding site for residue IOD A 315
13AD4SOFTWAREASP B:12 , GLY B:25 , GLY B:26 , GLY B:27 , TYR B:30 , TYR B:75 , GLN B:136 , ARG B:140 , ASP B:219 , HOH B:428binding site for residue INS B 301
14AD5SOFTWAREARG B:85 , HIS B:164 , ASP B:166 , SER B:187 , ASN B:188 , GLY B:189 , PHE B:204 , VAL B:207 , VAL B:209 , SER B:214 , ALA B:217 , GLY B:218 , THR B:245 , LEU B:249 , MG B:303 , HOH B:417 , HOH B:419 , HOH B:424 , HOH B:426 , HOH B:428 , HOH B:432binding site for residue ACP B 302
15AD6SOFTWAREGLN B:136 , ACP B:302 , HOH B:423 , HOH B:424 , HOH B:426 , HOH B:428binding site for residue MG B 303
16AD7SOFTWARETHR B:203binding site for residue IOD B 304
17AD8SOFTWAREARG B:11 , PRO B:51binding site for residue IOD B 305
18AD9SOFTWARESER B:123binding site for residue IOD B 306
19AE1SOFTWAREPRO B:144binding site for residue IOD B 307
20AE2SOFTWAREHOH B:415binding site for residue IOD B 308
21AE3SOFTWAREASP A:101 , IOD A:308 , IOD A:309 , LYS B:239binding site for residue IOD B 310
22AE4SOFTWAREGLU A:98 , LEU A:99 , PRO A:100 , GLN B:236binding site for residue IOD B 311
23AE5SOFTWAREASP B:182 , TYR B:229binding site for residue IOD B 312
24AE6SOFTWAREARG A:85 , TYR B:170binding site for residues IOD B 309 and IOD B 313

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XF7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XF7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XF7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XF7)

(-) Exons   (0, 0)

(no "Exon" information available for 4XF7)

(-) 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..eeeehhhhhh....ee.....ee.hhhh...eeeeehhhhh.ee..hhhhh.eeeee.....eeeee..eeeeee..........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xf7 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......eeeeeee...eeeeeeee..............eeee.......hhhhhhhhhhhh..eeeehhhhhh....ee.....ee.hhhh...eeeeehhhhh.ee..hhhhh.eeeeee..eeeeeee..eeeeee..........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xf7 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)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 4XF7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XF7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XF7)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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4xf7