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(-) Description

Title :  CRYSTAL STRUCTURE OF FLT3
 
Authors :  J. Griffith, J. Black, C. Faerman, L. Swenson, M. Wynn, F. Lu, J. Lippke, K. Saxena
Date :  19 Nov 03  (Deposition) - 03 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase, Structure, Autoinhibition, Juxtamembrane Domain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Griffith, J. Black, C. Faerman, L. Swenson, M. Wynn, F. Lu, J. Lippke, K. Saxena
The Structural Basis For Autoinhibition Of Flt3 By The Juxtamembrane Domain.
Mol. Cell V. 13 169 2004
PubMed-ID: 14759363  |  Reference-DOI: 10.1016/S1097-2765(03)00505-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FL CYTOKINE RECEPTOR
    ChainsA
    EC Number2.7.1.112
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System StrainHIGH-5 INSECT CELLS
    Expression System Taxid7111
    Expression System VectorPBEV10
    Expression System Vector TypeBACULOVIRUS
    FragmentCATALYTIC DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTYROSINE-PROTEIN KINASE RECEPTOR FLT3, STEM CELL TYROSINE KINASE 1, STK-1, CD135 ANTIGEN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1RJB)

(-) Sites  (0, 0)

(no "Site" information available for 1RJB)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RJB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RJB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric/Biological Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_065679D835EFLT3_HUMANUnclassified121913487AD835E
2UniProtVAR_065680D835HFLT3_HUMANUnclassified121913488AD835H
3UniProtVAR_065681D835NFLT3_HUMANUnclassified121913488AD835N
4UniProtVAR_065682D835VFLT3_HUMANUnclassified121909646AD835V
5UniProtVAR_065683D835YFLT3_HUMANUnclassified121913488AD835Y
6UniProtVAR_065684I836MFLT3_HUMANUnclassified121913232AI836M

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.FLT3_HUMAN616-644  1A:616-644
2RECEPTOR_TYR_KIN_IIIPS00240 Receptor tyrosine kinase class III signature.FLT3_HUMAN669-682  1A:669-682
3PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.FLT3_HUMAN807-819  1A:807-819

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002414531ENSE00001351959chr13:28674729-28674605125FLT3_HUMAN1-15150--
1.2ENST000002414532ENSE00000906615chr13:28644749-28644628122FLT3_HUMAN15-55410--
1.3ENST000002414533ENSE00000906614chr13:28636206-28636004203FLT3_HUMAN56-123680--
1.4ENST000002414534ENSE00000906613chr13:28631599-28631484116FLT3_HUMAN123-162400--
1.5ENST000002414535ENSE00000906612chr13:28626811-28626682130FLT3_HUMAN162-205440--
1.6ENST000002414536ENSE00000906611chr13:28624359-28624232128FLT3_HUMAN205-248440--
1.7ENST000002414537ENSE00000906610chr13:28623911-28623772140FLT3_HUMAN248-294470--
1.8ENST000002414538ENSE00000906609chr13:28623674-28623521154FLT3_HUMAN295-346520--
1.9ENST000002414539ENSE00000906608chr13:28622580-28622412169FLT3_HUMAN346-402570--
1.10ENST0000024145310ENSE00000827401chr13:28611425-28611322104FLT3_HUMAN402-437360--
1.11ENST0000024145311ENSE00000827402chr13:28610180-28610072109FLT3_HUMAN437-473370--
1.12ENST0000024145312ENSE00000827403chr13:28609810-28609632179FLT3_HUMAN473-533610--
1.13ENST0000024145313ENSE00000827404chr13:28608544-28608438107FLT3_HUMAN533-568360--
1.14ENST0000024145314ENSE00000827405chr13:28608351-28608219133FLT3_HUMAN569-613451A:572-61342
1.15ENST0000024145315ENSE00000827406chr13:28608128-28608024105FLT3_HUMAN613-648361A:613-64836
1.16ENST0000024145316ENSE00000827407chr13:28602425-28602315111FLT3_HUMAN648-685381A:648-685 (gaps)38
1.17ENST0000024145317ENSE00000827408chr13:28601378-28601225154FLT3_HUMAN685-736521A:685-71026
1.19ENST0000024145319ENSE00000827409chr13:28599080-2859899883FLT3_HUMAN736-764290--
1.20ENST0000024145320ENSE00000827410chr13:28597614-28597487128FLT3_HUMAN764-806431A:783-80624
1.21ENST0000024145321ENSE00000827411chr13:28592726-28592604123FLT3_HUMAN807-847411A:807-84741
1.22ENST0000024145322ENSE00000938491chr13:28589838-28589727112FLT3_HUMAN848-885381A:848-88538
1.23ENST0000024145323ENSE00000938492chr13:28589393-28589294100FLT3_HUMAN885-918341A:885-91834
1.24aENST0000024145324aENSE00000938493chr13:28588694-28588589106FLT3_HUMAN918-953361A:918-94730
1.26cENST0000024145326cENSE00001487116chr13:28578311-28577411901FLT3_HUMAN954-993400--

(-) 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:298
 aligned with FLT3_HUMAN | P36888 from UniProtKB/Swiss-Prot  Length:993

    Alignment length:376
                                   581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941      
           FLT3_HUMAN   572 YESQLQMVQVTGSSDNEYFYVDFREYEYDLKWEFPRENLEFGKVLGSGAFGKVMNATAYGISKTGVSIQVAVKMLKEKADSSEREALMSELKMMTQLGSHENIVNLLGACTLSGPIYLIFEYCCYGDLLNYLRSKREKFHRTWTEIFKEHNFSFYPTFQSHPNSSMPGSREVQIHPDSDQISGLHGNSFHSEDEIEYENQKRLEEEEDLNVLTFEDLLCFAYQVAKGMEFLEFKSCVHRDLAARNVLVTHGKVVKICDFGLARDIMSDSNYVVRGNARLPVKWMAPESLFEGIYTIKSDVWSYGILLWEIFSLGVNPYPGIPVDANFYKLIQNGFKMDQPFYATEEIYIIMQSCWAFDSRKRPSFPNLTSFLGCQL 947
               SCOP domains d1rjba_ A: Fl cytokine receptor                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1rjbA01 A:572-695 Phosphorylase Kinase; domain 1                                                                            1rjbA02 A:696-9                                                                        47 Transferase(Phosphotransferase) domain 1                                                                                                                           CATH domains
               Pfam domains --------------------------------------Pkinase_Tyr-1rjbA01 A:610-943                                                                                                                                                                                                                                                                                                                 ---- Pfam domains
         Sec.struct. author ....eeeeee.......eee.hhhhh..hhhhh.hhh.eeeeeeeee...eeeeeeeee.......eeeeeeeee..------hhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhh.....------------------------------------------------------------------------.hhhhhhhhhhhhhhhhhhhhhh.eee...hhh.eeee...eeee..hhhhhhhhhh...eee..eeehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh............hhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EM--------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H---------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N---------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
             SAPs(SNPs) (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V---------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (4)
             SAPs(SNPs) (5) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y---------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (5)
                    PROSITE --------------------------------------------PROTEIN_KINASE_ATP           ------------------------RECEPTOR_TYR_K----------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.14  PDB: A:572-613 UniProt: 569-613----------------------------------Exon 1.16  PDB: A:648-685 (gaps)      --------------------------------------------------Exon 1.19  PDB: -            ------------------------------------------Exon 1.21  PDB: A:807-847                Exon 1.22  PDB: A:848-885             --------------------------------Exon 1.24a  PDB: A:918-947     Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.15  PDB: A:613-648           ------------------------------------Exon 1.17  PDB: A:685-710 UniProt: 685-736          ---------------------------Exon 1.20  PDB: A:783-806 UniProt: 764-806 ------------------------------------------------------------------------------Exon 1.23  PDB: A:885-918         ----------------------------- Transcript 1 (2)
                 1rjb A 572 YESQLQMVQVTGSSDNEYFYVDFREYEYDLKWEFPRENLEFGKVLGSGAFGKVMNATAYGISKTGVSIQVAVKMLKE------REALMSELKMMTQLGSHENIVNLLGACTLSGPIYLIFEYCCYGDLLNYLRSKREKF------------------------------------------------------------------------LTFEDLLCFAYQVAKGMEFLEFKSCVHRDLAARNVLVTHGKVVKICDFGLARDIMSDSNYVVRGNARLPVKWMAPESLFEGIYTIKSDVWSYGILLWEIFSLGVNPYPGIPVDANFYKLIQNGFKMDQPFYATEEIYIIMQSCWAFDSRKRPSFPNLTSFLGCQL 947
                                   581       591       601       611       621       631       641      |  -   |   661       671       681       691       701        |-         -         -         -         -         -         -         - |     791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941      
                                                                                                      648    655                                                    710                                                                      783                                                                                                                                                                    

   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/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (50, 50)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FLT3_HUMAN | P36888)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004896    cytokine receptor activity    Combining with a cytokine and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    GO:0035259    glucocorticoid receptor binding    Interacting selectively and non-covalently with a glucocorticoid receptor.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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.
    GO:0004714    transmembrane receptor protein tyrosine kinase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
    GO:0005021    vascular endothelial growth factor-activated receptor activity    Combining with a vascular endothelial growth factor (VEGF) and transmitting the signal across the plasma membrane to initiate a change in cell activity.
biological process
    GO:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    GO:0031100    animal organ regeneration    The regrowth of a lost or destroyed animal organ.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0071345    cellular response to cytokine 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 cytokine stimulus.
    GO:0071385    cellular response to glucocorticoid 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 glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:0035726    common myeloid progenitor cell proliferation    The multiplication or reproduction of common myeloid progenitor cells, resulting in the expansion of a cell population. A common myeloid progenitor cell is a progenitor cell committed to the myeloid lineage.
    GO:0019221    cytokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0097028    dendritic cell differentiation    The process in which a precursor cell type acquires the specialized features of a dendritic cell. A dendritic cell is a leukocyte of dendritic lineage specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation.
    GO:0030097    hemopoiesis    The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
    GO:0001776    leukocyte homeostasis    The process of regulating the proliferation and elimination of cells of the immune system such that the total number of cells of a particular cell type within a whole or part of an organism is stable over time in the absence of an outside stimulus.
    GO:0046651    lymphocyte proliferation    The expansion of a lymphocyte population by cell division.
    GO:0002318    myeloid progenitor cell differentiation    The process in which a precursor cell type acquires the specialized features of a myeloid progenitor cell. Myeloid progenitor cells include progenitor cells for any of the myeloid lineages.
    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:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    GO:0043410    positive regulation of MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0043552    positive regulation of phosphatidylinositol 3-kinase activity    Any process that activates or increases the frequency, rate or extent of phosphatidylinositol 3-kinase activity.
    GO:0014068    positive regulation of phosphatidylinositol 3-kinase signaling    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:0042531    positive regulation of tyrosine phosphorylation of STAT protein    Any process that activates or increases the frequency, rate or extent of the introduction of a phosphate group to a tyrosine residue of a STAT (Signal Transducer and Activator of Transcription) protein.
    GO:0002328    pro-B cell differentiation    The process in which a precursor cell type acquires the specialized features of a pro-B cell. Pro-B cells are the earliest stage of the B cell lineage and undergo heavy chain D and J gene rearrangements, although they are not fully committed.
    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:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0010243    response to organonitrogen compound    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 organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
    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.
    GO:0038084    vascular endothelial growth factor signaling pathway    A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
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:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    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.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FLT3_HUMAN | P368883qs7 3qs9 4rt7 4xuf

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