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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHORYLATED HUMAN FELINE SARCOMA VIRAL ONCOGENE HOMOLOGUE (V-FES) IN COMPLEX WITH STAUROSPORINE AND A CONSENSUS PEPTIDE
 
Authors :  P. Filippakopoulos, E. Salah, C. Cooper, S. S. Picaud, J. M. Elkins, F. V C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, S. Knapp, Stru Genomics Consortium (Sgc)
Date :  26 Feb 08  (Deposition) - 25 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fes, V-Fes, Fujinami, Avian Sarcoma, Viral, Oncogene, Feline Sarcoma Virus, Active, Sgc, Structural Genomics Consortium, Atp-Binding, Kinase, Nucleotide-Binding, Phosphoprotein, Proto-Oncogene, Sh2 Domain, Transferase, Tyrosine-Protein Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Filippakopoulos, M. Kofler, O. Hantschel, G. D. Gish, F. Grebien, E. Salah, P. Neudecker, L. E. Kay, B. E. Turk, G. Superti-Furga, T. Pawson, S. Knapp
Structural Coupling Of Sh2-Kinase Domains Links Fes And Abl Substrate Recognition And Kinase Activation
Cell(Cambridge, Mass. ) V. 134 793 2008
PubMed-ID: 18775312  |  Reference-DOI: 10.1016/J.CELL.2008.07.047

(-) Compounds

Molecule 1 - PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FES/FPS
    ChainsA
    EC Number2.7.10.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3-YOP-PPASE
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 448-822
    GeneFES, FPS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymC-FES
 
Molecule 2 - SYNTHETIC PEPTIDE
    ChainsB
    EngineeredYES
    Other DetailsSYNTHETIC PEPTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CL2Ligand/IonCHLORIDE ION
3PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
4STU3Ligand/IonSTAUROSPORINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:766 , GLN A:767 , ARG A:770BINDING SITE FOR RESIDUE CL A 904
2AC3SOFTWAREILE A:567 , GLY A:568 , ARG A:569 , ALA A:588 , GLU A:607 , MET A:636 , GLU A:637 , LEU A:638 , GLY A:642 , ASP A:643 , ARG A:687 , LEU A:690 , SER A:700 , ASP A:701BINDING SITE FOR RESIDUE STU A 901
3AC4SOFTWAREASP A:583 , THR A:585 , ARG A:621 , LEU A:622 , ILE A:623BINDING SITE FOR RESIDUE STU A 902
4AC5SOFTWAREHIS A:456 , LYS A:553 , TRP A:554 , GLU A:559 , ARG A:581BINDING SITE FOR RESIDUE STU A 903

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CD3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:630 -Pro A:631

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CD3)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.FES_HUMAN460-549  1A:460-549
2PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.FES_HUMAN567-590  1A:567-590
3PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.FES_HUMAN679-691  1A:679-691

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003288502aENSE00001925529chr15:91427642-91427774133FES_HUMAN-00--
1.4bENST000003288504bENSE00002144049chr15:91428267-91428488222FES_HUMAN1-71710--
1.4hENST000003288504hENSE00001297839chr15:91428642-91428815174FES_HUMAN72-129580--
1.5bENST000003288505bENSE00001726182chr15:91430191-9143028797FES_HUMAN130-162330--
1.6aENST000003288506aENSE00001669837chr15:91430417-91430600184FES_HUMAN162-223620--
1.7bENST000003288507bENSE00001772963chr15:91432536-91432673138FES_HUMAN223-269470--
1.7cENST000003288507cENSE00001641844chr15:91432747-91432866120FES_HUMAN269-309410--
1.8cENST000003288508cENSE00001731816chr15:91433070-91433192123FES_HUMAN309-350420--
1.9ENST000003288509ENSE00001745690chr15:91433322-91433508187FES_HUMAN350-412630--
1.10cENST0000032885010cENSE00001734229chr15:91433631-9143371484FES_HUMAN413-440280--
1.11cENST0000032885011cENSE00001292079chr15:91434212-91434421210FES_HUMAN441-510701A:446-506 (gaps)61
1.12bENST0000032885012bENSE00001806076chr15:91434784-91434906123FES_HUMAN511-551411A:511-551 (gaps)41
1.13aENST0000032885013aENSE00001605790chr15:91435288-9143534154FES_HUMAN552-569181A:552-56918
1.14ENST0000032885014ENSE00001623952chr15:91435937-91436055119FES_HUMAN570-609401A:570-609 (gaps)40
1.15aENST0000032885015aENSE00001320193chr15:91436330-9143642495FES_HUMAN609-641331A:609-64133
1.16bENST0000032885016bENSE00001302270chr15:91436521-91436644124FES_HUMAN641-682421A:641-68242
1.17ENST0000032885017ENSE00001685092chr15:91436884-91437041158FES_HUMAN682-735541A:682-73554
1.18ENST0000032885018ENSE00001802839chr15:91437166-91437288123FES_HUMAN735-776421A:735-77642
1.19fENST0000032885019fENSE00001313735chr15:91438646-91439006361FES_HUMAN776-822471A:776-82146

(-) 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:353
 aligned with FES_HUMAN | P07332 from UniProtKB/Swiss-Prot  Length:822

    Alignment length:376
                                   455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815      
            FES_HUMAN   446 QLIPEVQKPLHEQLWYHGAIPRAEVAELLVHSGDFLVRESQGKQEYVLSVLWDGLPRHFIIQSLDNLYRLEGEGFPSIPLLIDHLLSTQQPLTKKSGVVLHRAVPKDKWVLNHEDLVLGEQIGRGNFGEVFSGRLRADNTLVAVKSCRETLPPDLKAKFLQEARILKQYSHPNIVRLIGVCTQKQPIYIVMELVQGGDFLTFLRTEGARLRVKTLLQMVGDAAAGMEYLESKCCIHRDLAARNCLVTEKNVLKISDFGMSREEADGVYAASGGLRQVPVKWTAPEALNYGRYSSESDVWSFGILLWETFSLGASPYPNLSNQQTREFVEKGGRLPCPELCPDAVFRLMEQCWAYEPGQRPSFSTIYQELQSIRKRH 821
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cd3A01 A:446-541 SHC Adaptor Protein                                                           -----------3cd3A02 A:553-642 Phosphorylase Kinase; d    omain 1                                      3cd3A03 A:643-821 Transferase(Phosphotransferase) domain 1                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.......hhhhhhhhh....eeeeee.---..eeee.-----..eeee----.....----..hhhhhhhhhhhhh...---......ee........hhh.eeeeeeeee....eeeeeee.....eeeeee..----hhhhhhhhhhhhhhh.........eeeee......eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee....eee.....eeee.hhhhhhhhhhheeehhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------SH2  PDB: A:460-549 UniProt: 460-549                                                      -----------------PROTEIN_KINASE_ATP      ----------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11c  PDB: A:446-506 (gaps) UniProt: 441-510 [INCOMPLETE]  Exon 1.12b  PDB: A:511-551 (gaps)        Exon 1.13a        Exon 1.14  PDB: A:570-609 (gaps)        -------------------------------Exon 1.16b  PDB: A:641-682                ----------------------------------------------------Exon 1.18  PDB: A:735-776 UniProt: 735-776--------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.15a  PDB: A:609-641       ----------------------------------------Exon 1.17  PDB: A:682-735 UniProt: 682-735            ----------------------------------------Exon 1.19f  PDB: A:776-821 UniProt: 776-822    Transcript 1 (2)
                 3cd3 A 446 SMIPEVQKPLHEQLWYHGAIPRAEVAELLVHSGDFLVRES---QEYVLSV-----PRHFII----NLYRL----FPSIPLLIDHLLSTQQPL---SGVVLHRAVPKDKWVLNHEDLVLGEQIGRGNFGEVFSGRLRADNTLVAVKSCR----PDLKAKFLQEARILKQYSHPNIVRLIGVCTQKQPIYIVMELVQGGDFLTFLRTEGARLRVKTLLQMVGDAAAGMEYLESKCCIHRDLAARNCLVTEKNVLKISDFGMSREEADGVyAASGGLRQVPVKWTAPEALNYGRYSSESDVWSFGILLWETFSLGASPYPNLSNQQTREFVEKGGRLPCPELCPDAVFRLMEQCWAYEPGQRPSFSTIYQELQSIRKRH 821
                                   455       465       475       485   |   495     | 505|    | 515    |  525       535 |   | 545       555       565       575       585       | -  |    605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815      
                                                                 485 489   495   501  506  511 515  520              537 541                                                 593  598                                                                                                                713-PTR                                                                                                        

Chain B from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..eeee Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 3cd3 B   0 xIYESL   5
                            |     
                            0-ACE 

   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 3CD3)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CD3)

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FES_HUMAN | P07332)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0034987    immunoglobulin receptor binding    Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    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:0035091    phosphatidylinositol binding    Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    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: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:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0007173    epidermal growth factor receptor signaling pathway    A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0001578    microtubule bundle formation    A process that results in a parallel arrangement of microtubules.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    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:2000251    positive regulation of actin cytoskeleton reorganization    Any process that activates or increases the frequency, rate or extent of actin cytoskeleton reorganization.
    GO:0031116    positive regulation of microtubule polymerization    Any process that activates or increases the frequency, rate or extent of microtubule polymerization.
    GO:0045639    positive regulation of myeloid cell differentiation    Any process that activates or increases the frequency, rate or extent of myeloid cell differentiation.
    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:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    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:0045595    regulation of cell differentiation    Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features.
    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:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0043304    regulation of mast cell degranulation    Any process that modulates the frequency, rate, or extent of mast cell degranulation.
    GO:0060627    regulation of vesicle-mediated transport    Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0015630    microtubule cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FES_HUMAN | P073321wqu 2dcr 3bkb 3cbl 4dyl 4e93

(-) Related Entries Specified in the PDB File

3cbl CRYSTAL STRUCTURE OF HUMAN FELINE SARCOMA VIRAL ONCOGENE HOMOLOGUE (V-FES) IN COMPLEX WITH STAUROSPORINE AND A CONSENSUS PEPTIDE