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(-) Description

Title :  THE CRYSTAL STRUCTURE OF HUMAN ABL2 IN COMPLEX WITH GLEEVEC
 
Authors :  E. Ugochukwu, E. Salah, A. Barr, P. Mahajan, B. Shrestha, P. Savitsky, A. Chaikuad, P. Filippakopoulos, A. Roos, A. C. W. Pike, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, S. Knapp, Struct Genomics Consortium (Sgc)
Date :  31 Mar 09  (Deposition) - 21 Apr 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Tyrosine Kinase, Abl, Abelson Murine Leukemia Viral Oncogene, Atp- Binding, Cell Adhesion, Cytoskeleton, Kinase, Lipoprotein, Magnesium, Manganese, Metal-Binding, Myristate, Nucleotide-Binding, Phosphoprotein, Sh2 Domain, Sh3 Domain, Transferase, Tyrosine- Protein Kinase, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Salah, E. Ugochukwu, A. Barr, P. Mahajan, B. Shrestha, P. Savitsky, S. Knapp
The Crystal Structure Of Human Abl2 In Complex With Gleevec
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE ABL2
    ChainsA
    EC Number2.7.10.2
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Cell LineHIGH5 INSECT CELL
    Expression System CommonCABBAGE LOOPER
    Expression System PlasmidPFB-LIC-BSE
    Expression System Taxid7111
    Expression System Vector TypeBACULOVIRUS
    FragmentPROTEIN KINASE
    GeneABL2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymABELSON MURINE LEUKEMIA VIRAL ONCOGENE HOMOLOG 2, ABELSON- RELATED GENE PROTEIN, TYROSINE KINASE ARG

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1STI2Ligand/Ion4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1STI2Ligand/Ion4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1STI4Ligand/Ion4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:73 , VAL A:302 , ALA A:315 , LYS A:317 , GLU A:332 , MET A:336 , VAL A:345 , ILE A:359 , THR A:361 , TYR A:363 , MET A:364 , ILE A:406 , HIS A:407 , ALA A:426 , ASP A:427 , PHE A:428BINDING SITE FOR RESIDUE STI A 1001
2AC2SOFTWAREHOH A:30 , HOH A:53 , ALA A:383 , VAL A:384 , LEU A:387 , TYR A:388 , GLU A:508 , GLY A:509 , PRO A:511 , VAL A:514 , HOH A:549BINDING SITE FOR RESIDUE STI A 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro A:355 -Pro A:356

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_055413R519IABL2_HUMANUnclassified  ---AR519I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_055413R519IABL2_HUMANUnclassified  ---AR519I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_055413R519IABL2_HUMANUnclassified  ---AR519I

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.ABL2_HUMAN294-317  1A:294-317
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.ABL2_HUMAN405-417  1A:405-417
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.ABL2_HUMAN294-317  1A:294-317
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.ABL2_HUMAN405-417  1A:405-417
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.ABL2_HUMAN294-317  2A:294-317
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.ABL2_HUMAN405-417  2A:405-417

(-) Exons   (0, 0)

(no "Exon" information available for 3GVU)

(-) 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:271
 aligned with ABL2_HUMAN | P42684 from UniProtKB/Swiss-Prot  Length:1182

    Alignment length:323
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543   
           ABL2_HUMAN   224 TTADGKVYVTAESRFSTLAELVHHHSTVADGLVTTLHYPAPKCNKPTVYGVSPIHDKWEMERTDITMKHKLGGGQYGEVYVGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTLEPPFYIVTEYMPYGNLLDYLRECNREEVTAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHVVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNTFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYDLLEKGYRMEQPEGCPPKVYELMRACWKWSPADRPSFAETHQAFETMFHDS 546
               SCOP domains d3gv                               ua_ A              : automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh-------------------------------hhh..--------------......hhh.eeeeee.hhhh...eeeeee.hhheeeeeeee.....hhhhhhhhhhhhh.........eeeee.....eeeeee.....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.hhh.eee.......---......----..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I--------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gvu A 269 GTEN-------------------------------LYFQS--------------MDKWEMERTDITMKHKLGGGQYGEVYVGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTLEPPFYIVTEYMPYGNLLDYLRECNREEVTAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHVVKVADFGLSR---GDTYTA----KFPIKWTAPESLAYNTFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYDLLEKGYRMEQPEGCPPKVYELMRACWKWSPADRPSFAETHQAFETMFHDS 546
                               |     -         -         -     | 277         -    |  283       293       303       313       323       333       343       353       363       373       383       393       403       413       423        |-  |    | -  |    453       463       473       483       493       503       513       523       533       543   
                             272                             273 277            278                                                                                                                                                       432 436  441  446                                                                                                    

   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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (41, 41)

Asymmetric Unit(hide GO term definitions)
Chain A   (ABL2_HUMAN | P42684)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0051015    actin filament binding    Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
    GO:0003785    actin monomer binding    Interacting selectively and non-covalently with monomeric actin, also known as G-actin.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004715    non-membrane spanning protein tyrosine kinase activity    Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    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:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0071300    cellular response to retinoic acid    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 retinoic acid stimulus.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0038083    peptidyl-tyrosine autophosphorylation    The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    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:0007204    positive regulation of cytosolic calcium ion concentration    Any process that increases the concentration of calcium ions in the cytosol.
    GO:0010976    positive regulation of neuron projection development    Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0051353    positive regulation of oxidoreductase activity    Any process that activates or increases the frequency, rate or extent of oxidoreductase activity, the 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.
    GO:0010863    positive regulation of phospholipase C activity    Any process that increases the rate of phospholipase C activity.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:2000249    regulation of actin cytoskeleton reorganization    Any process that modulates the frequency, rate or extent of actin cytoskeleton reorganization.
    GO:0010506    regulation of autophagy    Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:0030155    regulation of cell adhesion    Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix.
    GO:2000145    regulation of cell motility    Any process that modulates the frequency, rate or extent of cell motility.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0030100    regulation of endocytosis    Any process that modulates the frequency, rate or extent of endocytosis.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007169    transmembrane receptor protein tyrosine kinase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.

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 Related Entries

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

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        ABL2_HUMAN | P426842ecd 2kk1 2xyn 3hmi 3ulr 4eih

(-) Related Entries Specified in the PDB File

1fpu CRYSTAL STRUCTURE OF ABL KINASE DOMAIN IN COMPLEX WITH A SMALL MOLECULE INHIBITOR