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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FLT3 LIGAND
 
Authors :  S. N. Savvides, T. Boone, P. A. Karplus
Date :  12 Apr 00  (Deposition) - 14 Jun 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 4:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Four-Helix Bundle, Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. N. Savvides, T. Boone, P. Andrew Karplus
Flt3 Ligand Structure And Unexpected Commonalities Of Helical Bundles And Cystine Knots.
Nat. Struct. Biol. V. 7 486 2000
PubMed-ID: 10881197  |  Reference-DOI: 10.1038/75896
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FLT3 LIGAND
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemBACTERIA
    Expression System CommonEUBACTERIA
    Expression System Taxid2
    FragmentRECEPTOR BINDING DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD
Biological Unit 3 (1x)A (1x)B (1x)C (1x)D (1x)
Biological Unit 4 (1x)A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1ZN9Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:58 , HIS A:80 , HOH A:4067 , HOH A:4068BINDING SITE FOR RESIDUE ZN A 135
2AC2SOFTWAREHIS A:8 , GLU C:129BINDING SITE FOR RESIDUE ZN A 136
3AC3SOFTWAREASP A:3 , ASP C:3BINDING SITE FOR RESIDUE ZN A 137
4AC4SOFTWAREHIS B:80 , GLU B:110BINDING SITE FOR RESIDUE ZN B 1135
5AC5SOFTWARESER B:12 , ASP B:14 , LYS B:18 , GLU B:78BINDING SITE FOR RESIDUE ZN B 1136
6AC6SOFTWAREGLN B:2 , ASP B:40 , GLU B:42 , HOH B:5017 , HIS C:8BINDING SITE FOR RESIDUE ZN B 1137
7AC7SOFTWAREGLU C:58 , HIS C:80 , HOH C:6033BINDING SITE FOR RESIDUE ZN C 2135
8AC8SOFTWAREPRO B:134 , SER C:12 , ASP C:14 , LYS C:18 , GLU C:78 , HOH C:6042BINDING SITE FOR RESIDUE ZN C 2136
9AC9SOFTWAREGLU D:58 , HIS D:80BINDING SITE FOR RESIDUE ZN D 3135

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:4 -A:85
2A:44 -A:127
3A:93 -A:132
4B:4 -B:85
5B:44 -B:127
6B:93 -B:132
7C:4 -C:85
8C:44 -C:127
9C:93 -C:132
10D:4 -D:85
11D:44 -D:127
12D:93 -D:132

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ETE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ETE)

(-) Exons   (0, 0)

(no "Exon" information available for 1ETE)

(-) 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:134
 aligned with FLT3L_HUMAN | P49771 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:134
                                    36        46        56        66        76        86        96       106       116       126       136       146       156    
          FLT3L_HUMAN    27 TQDCSFQHSPISSDFAVKIRELSDYLLQDYPVTVASNLQDEELCGGLWRLVLAQRWMERLKTVAGSKMQGLLERVNTEIHFVTKCAFQPPPSCLRFVQTNISRLLQETSEQLVALKPWITRQNFSRCLELQCQP 160
               SCOP domains d1etea_ A: Flt3 ligand                                                                                                                 SCOP domains
               CATH domains 1eteA00 A:1-134  [code=1.20.1250.10, no name defined]                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhh......eeeee........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..........eeeeehhhhhhhhhhhhhhhh.......hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ete A   1 TQDCSFQHSPISSDFAVKIRELSDYLLQDYPVTVASNLQDDELCGGLWRLVLAQRWMERLKTVAGSKMQGLLERVNTEIHFVTKCAFQPPPSCLRFVQTNISRLLQETSEQLVALKPWITRQNFSRCLELQCQP 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    

Chain B from PDB  Type:PROTEIN  Length:134
 aligned with FLT3L_HUMAN | P49771 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:134
                                    36        46        56        66        76        86        96       106       116       126       136       146       156    
          FLT3L_HUMAN    27 TQDCSFQHSPISSDFAVKIRELSDYLLQDYPVTVASNLQDEELCGGLWRLVLAQRWMERLKTVAGSKMQGLLERVNTEIHFVTKCAFQPPPSCLRFVQTNISRLLQETSEQLVALKPWITRQNFSRCLELQCQP 160
               SCOP domains d1eteb_ B: Flt3 ligand                                                                                                                 SCOP domains
               CATH domains 1eteB00 B:1-134  [code=1.20.1250.10, no name defined]                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhh......eeeee........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..........eeeeehhhhhhhhhhhhhhhh.......hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ete B   1 TQDCSFQHSPISSDFAVKIRELSDYLLQDYPVTVASNLQDDELCGGLWRLVLAQRWMERLKTVAGSKMQGLLERVNTEIHFVTKCAFQPPPSCLRFVQTNISRLLQETSEQLVALKPWITRQNFSRCLELQCQP 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    

Chain C from PDB  Type:PROTEIN  Length:131
 aligned with FLT3L_HUMAN | P49771 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:131
                                    37        47        57        67        77        87        97       107       117       127       137       147       157 
          FLT3L_HUMAN    28 QDCSFQHSPISSDFAVKIRELSDYLLQDYPVTVASNLQDEELCGGLWRLVLAQRWMERLKTVAGSKMQGLLERVNTEIHFVTKCAFQPPPSCLRFVQTNISRLLQETSEQLVALKPWITRQNFSRCLELQC 158
               SCOP domains d1etec_ C: Flt3 ligand                                                                                                              SCOP domains
               CATH domains 1eteC00 C:2-132  [code=1.20.1250.10, no name defined]                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhh......eeeee........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..........eeeeehhhhhhhhhhhhhhhh.......hhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ete C   2 QDCSFQHSPISSDFAVKIRELSDYLLQDYPVTVASNLQDDELCGGLWRLVLAQRWMERLKTVAGSKMQGLLERVNTEIHFVTKCAFQPPPSCLRFVQTNISRLLQETSEQLVALKPWITRQNFSRCLELQC 132
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 

Chain D from PDB  Type:PROTEIN  Length:130
 aligned with FLT3L_HUMAN | P49771 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:130
                                    38        48        58        68        78        88        98       108       118       128       138       148       158
          FLT3L_HUMAN    29 DCSFQHSPISSDFAVKIRELSDYLLQDYPVTVASNLQDEELCGGLWRLVLAQRWMERLKTVAGSKMQGLLERVNTEIHFVTKCAFQPPPSCLRFVQTNISRLLQETSEQLVALKPWITRQNFSRCLELQC 158
               SCOP domains d1eted_ D: Flt3 ligand                                                                                                             SCOP domains
               CATH domains 1eteD00 D:3-132  [code=1.20.1250.10, no name defined]                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhh......eeeee........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..........eeeeehhhhhhhhhhhhhhh........hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ete D   3 DCSFQHSPISSDFAVKIRELSDYLLQDYPVTVASNLQDDELCGGLWRLVLAQRWMERLKTVAGSKMQGLLERVNTEIHFVTKCAFQPPPSCLRFVQTNISRLLQETSEQLVALKPWITRQNFSRCLELQC 132
                                    12        22        32        42        52        62        72        82        92       102       112       122       132

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ETE)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (FLT3L_HUMAN | P49771)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0030971    receptor tyrosine kinase binding    Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity.
biological process
    GO:0035162    embryonic hemopoiesis    The stages of blood cell formation that take place within the embryo.
    GO:0048873    homeostasis of number of cells within a tissue    Any biological process involved in the maintenance of the steady-state number of cells within a population of cells in a tissue.
    GO:0030098    lymphocyte differentiation    The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
    GO:0071866    negative regulation of apoptotic process in bone marrow    Any process that stops, prevents, or reduces the frequency, rate or extent of the occurrence or rate of cell death by apoptotic process in the bone marrow.
    GO:0045787    positive regulation of cell cycle    Any process that activates or increases the rate or extent of progression through the cell cycle.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0071864    positive regulation of cell proliferation in bone marrow    A process that activates or increases the frequency, rate or extent of cell proliferation in the bone marrow.
    GO:0045663    positive regulation of myoblast differentiation    Any process that activates or increases the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
    GO:1901741    positive regulation of myoblast fusion    Any process that activates or increases the frequency, rate or extent of myoblast fusion.
    GO:0032825    positive regulation of natural killer cell differentiation    Any process that activates or increases the frequency, rate or extent of natural killer cell differentiation.
    GO:0090290    positive regulation of osteoclast proliferation    Any process that increases the rate, frequency, or extent of the multiplication or reproduction of osteoclasts, resulting in the expansion of an osteoclast cell population.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0030885    regulation of myeloid dendritic cell activation    Any process that modulates the frequency or rate of myeloid dendritic cell activation.
    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.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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:0031233    intrinsic component of external side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that penetrate the external side of the plasma membrane only, either directly or via some covalently attached hydrophobic anchor.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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
        FLT3L_HUMAN | P497713qs7 3qs9

(-) Related Entries Specified in the PDB File

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