Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN FTO IN COMPLEX WITH SUBFAMILY-SELECTIVE INHIBITOR 12
 
Authors :  D. W. Toh, L. Sun, J. Tan, Y. Chen, L. Z. M. Lau, W. Hong, E. C. Y. Woon, Y. G. G
Date :  09 Apr 14  (Deposition) - 01 Oct 14  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Small Molecular Probe (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. W. Toh, L. Sun, L. Z. M. Lau, J. Tan, J. J. A. Low, W. Qiang, C. W. Q. Tang, J. Yi, E. J. Y. Cheong, M. J. H. Tan, Y. Chen, W. Hong, Y. G. Gao, E. C. Y. Woon
A Strategy Based On Nucleotide Specificity Leads To Subfamily-Selective And Cell-Active Inhibitor Of N6-Methyladenosine Demethylase Fto
Chem. Sci. V. 6 112 2015
PubMed: search  |  Reference-DOI: 10.1039/C4SC02554G

(-) Compounds

Molecule 1 - ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE FTO
    Chains: A
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET28B
    Expression System Vector Type: PLASMID
    Fragment: DEMETHYLASE, RESIDUES 32-505
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: FAT MASS AND OBESITY-ASSOCIATED PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
16MK1Ligand/Ion(2E)-4-[N'-(4-BENZYL-PYRIDINE-3-CARBONYL)-HYDRAZINO]-4-OXO-BUT-2-ENOIC ACID
2NI1Ligand/IonNICKEL (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:231 , ASP A:233 , HIS A:307 , ARG A:322 , 6MK A:1504 , HOH A:2030BINDING SITE FOR RESIDUE NI A1503
2AC2SOFTWARETYR A:106 , LEU A:203 , HIS A:231 , HIS A:232 , ASP A:233 , GLU A:234 , VAL A:244 , TYR A:295 , HIS A:307 , VAL A:309 , ARG A:316 , SER A:318 , ARG A:322 , NI A:1503 , HOH A:2012 , HOH A:2024 , HOH A:2030BINDING SITE FOR RESIDUE 6MK A1504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:473 -Pro A:474

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076423H271PFTO_HUMANUnclassified  ---AH271P
2UniProtVAR_063252R316QFTO_HUMANDisease (GDFD)121918214AR316Q
3UniProtVAR_075468S319FFTO_HUMANDisease (GDFD)  ---AS319F
4UniProtVAR_075469R322QFTO_HUMANDisease (GDFD)745616565AR322Q
5UniProtVAR_032078A405VFTO_HUMANPolymorphism16952624AA405V
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CXW)

(-) 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:431
 aligned with FTO_HUMAN | Q9C0B1 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:491
                                    21        31        41        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       371       381       391       401       411       421       431       441       451       461       471       481       491       501 
            FTO_HUMAN    12 REAKKLRLLEELEDTWLPYLTPKDDEFYQQWQLKYPKLILREASSVSEELHKEVQEAFLTLHKHGCLFRDLVRIQGKDLLTPVSRILIGNPGCTYKYLNTRLFTVPWPVKGSNIKHTEAEIAAACETFLKLNDYLQIETIQALEELAAKEKANEDAVPLCMSADFPRVGMGSSYNGQDEVDIKSRAAYNVTLLNFMDPQKMPYLKEEPYFGMGKMAVSWHHDENLVDRSAVAVYSYSCEGPEEESEDDSHLEGRDPDIWHVGFKISWDIETPGLAIPLHQGDCYFMLDDLNATHQHCVLAGSQPRFSSTHRVAECSTGTLDYILQRCQLALQNVCDDVDNDDVSLKSFEPAVLKQGEEIHNEVEFEWLRQFWFQGNRYRKCTDWWCQPMAQLEALWKKMEGVTNAVLHEVKREGLPVEQRNEILTAILASLTARQNLRREWHARCQSRIARTLPADQKPECRPYWEKDDASMPLPFDLTDIVSELRGQLLE 502
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---------------.ee.....hhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhh.........eeee..eeee...eeeeee....eee....eee.ee.....-----...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...--------------------------..hhhhhh....eeeeeee....---...........eeeeee..........eeeeeee..-----------........eeeeeee.......eeeeee....eeee..hhhhheeeeee.....eeeeeee.......hhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhh...................hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P--------------------------------------------Q--F--Q----------------------------------------------------------------------------------V------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cxw A  27 RG---------------SHMTPKDDEFYQQWQLKYPKLILREASSVSEELHKEVQEAFLTLHKHGCLFRDLVRIQGKDLLTPVSRILIGNPGCTYKYLNTRLFTVPWPVKG-----TEAEIAAACETFLKLNDYLQIETIQALEELAAKEK--------------------------DEVDIKSRAAYNVTLLNFMDPQK---LKEEPYFGMGKMAVSWHHDENLVDRSAVAVYSYSCE-----------LEGRDPDIWHVGFKISWDIETPGLAIPLHQGDCYFMLDDLNATHQHCVLAGSQPRFSSTHRVAECSTGTLDYILQRCQLALQNVCDDVDNDDVSLKSFEPAVLKQGEEIHNEVEFEWLRQFWFQGNRYRKCTDWWCQPMAQLEALWKKMEGVTNAVLHEVKREGLPVEQRNEILTAILASLTARQNLRREWHARCQSRIARTLPADQKPECRPYWEKDDASMPLPFDLTDIVSELRGQLLE 502
                             |       -       |31        41        51        61        71        81        91       101       111       121|     |131       141       151       161|        -         -       191       201       211   |   221       231       241        |-         -|      271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501 
                             |              29                                                                                          122   128                               162                        189                   211 215                                250         262                                                                                                                                                                                                                                                
                            28
   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 4CXW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FTO_HUMAN | Q9C0B1)
molecular function
    GO:0043734    DNA-N1-methyladenine dioxygenase activity    Catalysis of the oxidative demethylation of N1-methyladenine and N3-methylcytosine in DNA, with concomitant decarboxylation of 2-oxoglutarate and releases oxidized methyl group on N1-methyladenine and N3-methylcytosine as formaldehyde.
    GO:1990931    RNA N6-methyladenosine dioxygenase activity    Catalysis of the oxidative demethylation of N6-methyladenosine RNA, with concomitant decarboxylation of 2-oxoglutarate and releases oxidized methyl group on N6-methyladenosine as formaldehyde.
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0035516    oxidative DNA demethylase activity    Catalysis of the removal of the methyl group from one or more nucleotides within a DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.
    GO:0035515    oxidative RNA demethylase activity    Catalysis of the removal of a methyl group from one or more nucleosides within a RNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0006307    DNA dealkylation involved in DNA repair    The repair of alkylation damage, e.g. the removal of the alkyl group at the O6-position of guanine by O6-alkylguanine-DNA alkyltransferase (AGT).
    GO:0080111    DNA demethylation    The removal of a methyl group from one or more nucleotides within an DNA molecule.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0042245    RNA repair    Any process that results in the repair of damaged RNA.
    GO:0060612    adipose tissue development    The process whose specific outcome is the progression of adipose tissue over time, from its formation to the mature structure. Adipose tissue is specialized tissue that is used to store fat.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0070989    oxidative demethylation    The process of removing one or more methyl groups from a molecule, involving the oxidation (i.e. electron loss) of one or more atoms in the substrate.
    GO:0035552    oxidative single-stranded DNA demethylation    Removal of the methyl group from one or more nucleotides within a single-stranded DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.
    GO:0035553    oxidative single-stranded RNA demethylation    Removal of the methyl group from one or more nucleotides within a single-stranded RNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.
    GO:0090335    regulation of brown fat cell differentiation    Any process that modulates the rate, frequency, or extent of brown fat cell differentiation. Brown fat cell differentiation is the process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria.
    GO:0010883    regulation of lipid storage    Any process that modulates the rate, frequency or extent of lipid storage. Lipid storage is the accumulation and maintenance in cells or tissues of lipids, compounds soluble in organic solvents but insoluble or sparingly soluble in aqueous solvents. Lipid reserves can be accumulated during early developmental stages for mobilization and utilization at later stages of development.
    GO:0040014    regulation of multicellular organism growth    Any process that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size.
    GO:0044065    regulation of respiratory system process    Any process that modulates the frequency, rate or extent of a respiratory system process, an organ system process carried out by any of the organs or tissues of the respiratory system.
    GO:0070350    regulation of white fat cell proliferation    Any process that modulates the frequency, rate or extent of white fat cell proliferation.
    GO:0001659    temperature homeostasis    A homeostatic process in which an organism modulates its internal body temperature.
cellular component
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    6MK  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:473 - Pro A:474   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4cxw
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  FTO_HUMAN | Q9C0B1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.14.11.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  612938
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  FTO_HUMAN | Q9C0B1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        FTO_HUMAN | Q9C0B1: 3lfm 4cxx 4cxy 4idz 4ie0 4ie4 4ie5 4ie6 4ie7 4qho 4qkn 4zs2 4zs3 5dab 5f8p

(-) Related Entries Specified in the PDB File

4cxx CRYSTAL STRUCTURE OF HUMAN FTO IN COMPLEX WITH ACYLHYDRAZINE INHIBITOR 16
4cxy CRYSTAL STRUCTURE OF HUMAN FTO IN COMPLEX WITH ACYLHYDRAZINE INHIBITOR 21
4cxz OXIDOREDUCTASE COMPLEX 4
4cy0 OXIDOREDUCTASE COMPLEX 5