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(-) Description

Title :  X-RAY STRUCTURE OF KETOHEXOKINASE IN COMPLEX WITH A PYRIMIDOPYRIMIDINE ANALOG 3
 
Authors :  M. C. Abad
Date :  11 Jan 11  (Deposition) - 18 Jan 12  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ketohexokinase, Atp Binding, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. E. Maryanoff, J. C. O'Neill, D. F. Mccomsey, S. C. Yabut, D. K. Luci, A. D. Jordan, J. A. Masucci, W. J. Jones, M. C. Abad, A. C. Gibbs, I. Petrounia
Inhibitors Of Ketohexokinase: Discovery Of Pyrimidinopyrimidines With Specific Substitution That Complements The Atp-Binding Site.
Acs Med Chem Lett V. 2 538 2011
PubMed-ID: 24900346  |  Reference-DOI: 10.1021/ML200070G

(-) Compounds

Molecule 1 - KETOHEXOKINASE
    ChainsA, B
    EC Number2.7.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28S
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneKHK
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHEPATIC FRUCTOKINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2XNN2Ligand/IonN~8~-(CYCLOPROPYLMETHYL)-2-(2,6-DIAZASPIRO[3.3]HEPT-2-YL)-N~4~-[2-(METHYLSULFANYL)PHENYL]PYRIMIDO[5,4-D]PYRIMIDINE-4,8-DIAMINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:108 , GLY A:255 , ALA A:256 , GLY A:257 , ASP A:258BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREASN A:107 , ALA A:224 , ALA A:226 , GLU A:227 , GLY A:229 , ALA A:230 , PRO A:246 , VAL A:250 , THR A:253 , ALA A:256 , GLY A:257 , PHE A:260 , CYS A:282 , ASP B:27BINDING SITE FOR RESIDUE XNN A 302
3AC3SOFTWAREARG A:31 , HIS B:113 , ARG B:141 , LYS B:174 , ARG B:176BINDING SITE FOR RESIDUE SO4 B 301
4AC4SOFTWAREARG B:78 , ARG B:79 , PHE B:294BINDING SITE FOR RESIDUE SO4 B 302
5AC5SOFTWAREALA B:224 , ALA B:226 , GLU B:227 , GLY B:229 , PHE B:245 , PRO B:246 , PRO B:247 , VAL B:250 , THR B:253 , GLY B:257 , CYS B:282 , ALA B:285 , CYS B:289BINDING SITE FOR RESIDUE XNN B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QAI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QAI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric/Biological Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_006072G40RKHK_HUMANDisease (FRUCT)104893643A/BG40R
2UniProtVAR_006073A43TKHK_HUMANDisease (FRUCT)104893644A/BA43T
3UniProtVAR_006074V49IKHK_HUMANPolymorphism2304681A/BV49I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QAI)

(-) Exons   (8, 16)

Asymmetric/Biological Unit (8, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002605981bENSE00001938617chr2:27309650-27310219570KHK_HUMAN1-31312A:3-31
B:-1-31
29
33
1.3ENST000002605983ENSE00000932389chr2:27315200-27315316117KHK_HUMAN31-70402A:31-70
B:31-70
40
40
1.5bENST000002605985bENSE00000932386chr2:27317668-27317802135KHK_HUMAN70-115462A:70-115
B:70-115
46
46
1.6ENST000002605986ENSE00000932384chr2:27319597-2731966973KHK_HUMAN115-139252A:115-139
B:115-139
25
25
1.7bENST000002605987bENSE00000932382chr2:27320371-27320517147KHK_HUMAN140-188492A:140-188
B:140-188
49
49
1.8ENST000002605988ENSE00000932381chr2:27322064-2732215289KHK_HUMAN189-218302A:189-218
B:189-218
30
30
1.9bENST000002605989bENSE00000932379chr2:27322288-27322445158KHK_HUMAN218-271542A:218-271
B:218-271
54
54
1.10dENST0000026059810dENSE00001880745chr2:27322533-273236401108KHK_HUMAN271-298282A:271-298
B:271-298
28
28

(-) 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:296
 aligned with KHK_HUMAN | P50053 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:296
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292      
            KHK_HUMAN     3 EKQILCVGLVVLDVISLVDKYPKEDSEIRCLSQRWQRGGNASNSCTVLSLLGAPCAFMGSMAPGHVADFLVADFRRRGVDVSQVAWQSKGDTPSSCCIINNSNGNRTIVLHDTSLPDVSATDFEKVDLTQFKWIHIEGRNASEQVKMLQRIDAHNTRQPPEQKIRVSVEVEKPREELFQLFGYGDVVFVSKDVAKHLGFQSAEEALRGLYGRVRKGAVLVCAWAEEGADALGPDGKLLHSDAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFDGIV 298
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeeeee........eee..eeeeeeehhhhhhhhhhhhh...eeee.ee..hhhhhhhhhhhhhh.......ee.......eeeeeee.....eeeeee.......hhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhh.......eeeeee...hhhhhhhhhh..eeeehhhhhhhh...hhhhhhhhhhhhh....eeeee.hhh.eeee.....eeee............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------R--T-----I--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:3-31       --------------------------------------Exon 1.5b  PDB: A:70-115 UniProt: 70-115      ------------------------Exon 1.7b  PDB: A:140-188 UniProt: 140-188       Exon 1.8  PDB: A:189-218      ----------------------------------------------------Exon 1.10d  PDB: A:271-298   Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.3  PDB: A:31-70 UniProt: 31-70   --------------------------------------------Exon 1.6  PDB: A:115-139 ------------------------------------------------------------------------------Exon 1.9b  PDB: A:218-271 UniProt: 218-271            --------------------------- Transcript 1 (2)
                 3qai A   3 GSQILCVGLVVLDVISLVDKYPKEDSEIRCLSQRWQRGGNASNSCTVLSLLGAPCAFMGSMAPGHVADFLVADFRRRGVDVSQVAWQSKGDTPSSCCIINNSNGNRTIVLHDTSLPDVSATDFEKVDLTQFKWIHIEGRNASEQVKMLQRIDAHNTRQPPEQKIRVSVEVEKPREELFQLFGYGDVVFVSKDVAKHLGFQSAEEALRGLYGRVRKGAVLVCAWAEEGADALGPDGKLLHSDAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFDGIV 298
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292      

Chain B from PDB  Type:PROTEIN  Length:301
 aligned with KHK_HUMAN | P50053 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:301
                             1  4  5                                                                                                                                                                                                                                                                                                     
                             |  |  | 7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297 
            KHK_HUMAN     - -MEEK--QILCVGLVVLDVISLVDKYPKEDSEIRCLSQRWQRGGNASNSCTVLSLLGAPCAFMGSMAPGHVADFLVADFRRRGVDVSQVAWQSKGDTPSSCCIINNSNGNRTIVLHDTSLPDVSATDFEKVDLTQFKWIHIEGRNASEQVKMLQRIDAHNTRQPPEQKIRVSVEVEKPREELFQLFGYGDVVFVSKDVAKHLGFQSAEEALRGLYGRVRKGAVLVCAWAEEGADALGPDGKLLHSDAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFDGIV 298
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...eeeeeeee........eee..eeeeeeehhhhhhhhhhhhh...eeee.ee..hhhhhhhhhhhhhh.......ee.......eeeeeee.....eeeee........hhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhh..eeeehhhhhhhh...hhhhhhhhhhhhh....eeeee.hhh.eeee.....eeee............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------R--T-----I--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) -Exon 1.1b  PDB: B:-1-31          --------------------------------------Exon 1.5b  PDB: B:70-115 UniProt: 70-115      ------------------------Exon 1.7b  PDB: B:140-188 UniProt: 140-188       Exon 1.8  PDB: B:189-218      ----------------------------------------------------Exon 1.10d  PDB: B:271-298   Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.3  PDB: B:31-70 UniProt: 31-70   --------------------------------------------Exon 1.6  PDB: B:115-139 ------------------------------------------------------------------------------Exon 1.9b  PDB: B:218-271 UniProt: 218-271            --------------------------- Transcript 1 (2)
                 3qai B  -2 GLVPRGSQILCVGLVVLDVISLVDKYPKEDSEIRCLSQRWQRGGNASNSCTVLSLLGAPCAFMGSMAPGHVADFLVADFRRRGVDVSQVAWQSKGDTPSSCCIINNSNGNRTIVLHDTSLPDVSATDFEKVDLTQFKWIHIEGRNASEQVKMLQRIDAHNTRQPPEQKIRVSVEVEKPREELFQLFGYGDVVFVSKDVAKHLGFQSAEEALRGLYGRVRKGAVLVCAWAEEGADALGPDGKLLHSDAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFDGIV 298
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297 

   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 3QAI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QAI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QAI)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KHK_HUMAN | P50053)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004454    ketohexokinase activity    Catalysis of the reaction: ATP + D-fructose = ADP + D-fructose 1-phosphate.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0046835    carbohydrate phosphorylation    The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y.
    GO:0061624    fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate    The chemical reactions and pathways resulting in the breakdown of fructose that results in the formation of dihydroxyacetone phosphate and glyceraldehyde-3-phosphate.
    GO:0006000    fructose metabolic process    The chemical reactions and pathways involving fructose, the ketohexose arabino-2-hexulose. Fructose exists in a open chain form or as a ring compound. D-fructose is the sweetest of the sugars and is found free in a large number of fruits and honey.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0009750    response to fructose    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fructose stimulus.
    GO:0009749    response to glucose    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
    GO:0032868    response to insulin    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0009744    response to sucrose    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a sucrose stimulus.
    GO:0010043    response to zinc ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a zinc ion stimulus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KHK_HUMAN | P500532hlz 2hqq 2hw1 3b3l 3nbv 3nbw 3nc2 3nc9 3nca 3q92 3qa2 3ro4

(-) Related Entries Specified in the PDB File

3nbv KETOHEXOKINASE IN COMPLEX WITH AMP-PNP AND FRUCTOSE
3nbw KETOHEXOKINASE IN COMPLEX WITH A PYRAZOLE COMPOUND
3nc2 KETOHEXOKINASE WITH A QUINAZOLINE COMPOUND
3nc9 KETOHEXOKINASE IN COMPLEX WITH AN INDAZOLE COMPOUND
3nca KETOHEXOKINASE IN COMPLEX WITH A THIENO PYRIDINOL COMPOUND
3q92 KETOHEXOKINASE IN COMPLEX WITH A PYRIMIDOPYRIMIDINE ANALOG 1
3qa2 KETOHEXOKINASE IN COMPLEX WITH A PYRIMIDOPYRIMIDINE ANALOG 2