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(-) Description

Title :  2:2 COMPLEX OF G-CSF WITH ITS RECEPTOR
 
Authors :  M. Aritomi, N. Kunishima, T. Okamoto, R. Kuroki, Y. Ota, K. Morikawa
Date :  08 Mar 99  (Deposition) - 08 Mar 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Class1 Cytokine, Hematopoietic Receptor, Signal Transduction, Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Aritomi, N. Kunishima, T. Okamoto, R. Kuroki, Y. Ota, K. Morikawa
Atomic Structure Of The Gcsf-Receptor Complex Showing A New Cytokine-Receptor Recognition Scheme.
Nature V. 401 713 1999
PubMed-ID: 10537111  |  Reference-DOI: 10.1038/44394

(-) Compounds

Molecule 1 - PROTEIN (GRANULOCYTE COLONY-STIMULATING FACTOR)
    Cellular LocationEXTRACELLULAR
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymG-CSF
 
Molecule 2 - PROTEIN (G-CSF RECEPTOR)
    Cellular LocationCELLULAR MEMBRANE
    ChainsB, D
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cellular LocationNUCLEUS
    Expression System Cell LineSF-9
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System VectorAUTOGRAPHA CALIFORNICA NUCLEAR POLYHEDROSIS VIRUS
    Expression System Vector TypeVIRUS
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsN-LINKED GLYCOSYLATION AT B10
    SynonymG-CSF-R

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:10 , GLN B:25BINDING SITE FOR RESIDUE NAG B 323
2AC2SOFTWAREASN D:10 , GLN D:25BINDING SITE FOR RESIDUE NAG D 923

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1A:37 -A:43
2A:65 -A:75
3B:13 -B:24
4B:49 -B:100
5B:59 -B:68
6B:130 -B:177
7B:148 -B:191
8C:37 -C:43
9C:65 -C:75
10D:13 -D:24
11D:49 -D:100
12D:59 -D:68
13D:130 -D:177
14D:148 -D:191

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CD9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric/Biological Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013073L157MCSF3_HUMANPolymorphism2227329A/CL125M
2UniProtVAR_013074A174TCSF3_HUMANPolymorphism2227330A/CA142T

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

(-) PROSITE Motifs  (2, 6)

Asymmetric/Biological Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTERLEUKIN_6PS00254 Interleukin-6 / G-CSF / MGF signature.CSF3_HUMAN97-122
 
  2A:65-90
C:65-90
2FN3PS50853 Fibronectin type-III domain profile.CSF3R_MOUSE126-231
 
236-331
 
434-529
334-433
530-624
  4B:7-112
D:7-112
B:117-212
D:117-212
-
-
-

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002254741bENSE00001309996chr17:38171697-3817176771CSF3_HUMAN1-14140--
1.1fENST000002254741fENSE00000950689chr17:38171944-38172107164CSF3_HUMAN14-68552A:5-36
C:7-36
32
30
1.2aENST000002254742aENSE00000950690chr17:38172486-38172593108CSF3_HUMAN69-104362A:37-72
C:37-72
36
36
1.2cENST000002254742cENSE00000950691chr17:38172738-38172884147CSF3_HUMAN105-153492A:73-121
C:73-121
49
49
1.3cENST000002254743cENSE00001268721chr17:38173048-381740661019CSF3_HUMAN154-207542A:122-175
C:122-175
54
54

(-) 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:171
 aligned with CSF3_HUMAN | P09919 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:174
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203    
           CSF3_HUMAN    34 GPASSLPQSFLLKCLEQVRKIQGDGAALQEKLVSECATYKLCHPEELVLLGHSLGIPWAPLSSCPSQALQLAGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQMEELGMAPALQPTQGAMPAFASAFQRRAGGVLVASHLQSFLEVSYRVLRHLAQP 207
               SCOP domains d1cd9a_ A: Granulocyte-colony st   imulating factor (G-CSF)                                                                                                                    SCOP domains
               CATH domains 1cd9A00 A:5-175  [code=1.20.1250   .10, no name defined]                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhh---hhhh...hhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------M----------------T--------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------INTERLEUKIN_6  PDB: A:65-9------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1f  PDB: A:5-36 [INCOMPLETE]Exon 1.2a  PDB: A:37-72             Exon 1.2c  PDB: A:73-121 UniProt: 105-153        Exon 1.3c  PDB: A:122-175 UniProt: 154-207             Transcript 1
                 1cd9 A   5 GPASSLPQSFLLKCLEQVRKIQGDGAALQEKL---CATYKLCHPEELVLLGHSLGIPWAPLSSCPSQALQLAGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQMEELGMAPALQPTQGAMPAFASAFQRRAGGVLVASHLQSFLEVSYRVLRHLAQP 175
                                    14        24        34 |   |  41        51        61        71        81        91       101       111       121       131       141       151       161       171    
                                                          36  37                                                                                                                                          

Chain B from PDB  Type:PROTEIN  Length:206
 aligned with CSF3R_MOUSE | P40223 from UniProtKB/Swiss-Prot  Length:837

    Alignment length:213
                                   129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329   
          CSF3R_MOUSE   120 AGYPPASPSNLSCLMHLTTNSLVCQWEPGPETHLPTSFILKSFRSRADCQYQGDTIPDCVAKKRQNNCSIPRKNLLLYQYMAIWVQAENMLGSSESPKLCLDPMDVVKLEPPMLQALDIGPDVVSHQPGCLWLSWKPWKPSEYMEQECELRYQPQLKGANWTLVFHLPSSKDQFELCGLHQAPVYTLQMRCIRSSLPGFWSPWSPGLQLRPTM 332
               SCOP domains d1cd9b1 B:1-107 Granulocyte colony-stimulating factor (GC-SF) receptor                                     d1cd9b2 B:10       8-213 Granulocyte colony-stimulating factor (GC-SF) receptor                            SCOP domains
               CATH domains 1cd9B01 B:1-108 Immunoglobulins                                                                             1cd9B02 B:1       09-213 Immunoglobulins                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeee....eeeeeee.........eeeeeeee.hhhhh....eeeeee......eeeee.hhh.....eeeeeeeee..eeee...eeehhhhh......eeeee..-------....eeeeee.hhhhh...eeeeeeeee.......eeeeeee..eeeeee........eeeeeeeee.............eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------FN3  PDB: B:7-112 UniProt: 126-231                                                                        ----FN3  PDB: B:117-212 UniProt: 236-331                                                            - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cd9 B   1 AGYPPASPSNLSCLMHLTTNSLVCQWEPGPETHLPTSFILKSFRSRADCQYQGDTIPDCVAKKRQNNCSIPRKNLLLYQYMAIWVQAENMLGSSESPKLCLDPMDVVKLEPPMLQALDI-------QPGCLWLSWKPWKPSEYMEQECELRYQPQLKGANWTLVFHLPSSKDQFELCGLHQAPVYTLQMRCIRSSLPGFWSPWSPGLQLRPTM 213
                                    10        20        30        40        50        60        70        80        90       100       110        |-      |130       140       150       160       170       180       190       200       210   
                                                                                                                                                119     127                                                                                      

Chain C from PDB  Type:PROTEIN  Length:169
 aligned with CSF3_HUMAN | P09919 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:172
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205  
           CSF3_HUMAN    36 ASSLPQSFLLKCLEQVRKIQGDGAALQEKLVSECATYKLCHPEELVLLGHSLGIPWAPLSSCPSQALQLAGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQMEELGMAPALQPTQGAMPAFASAFQRRAGGVLVASHLQSFLEVSYRVLRHLAQP 207
               SCOP domains d1cd9c_ C: Granulocyte-colony    stimulating factor (G-CSF)                                                                                                                  SCOP domains
               CATH domains 1cd9C00 C:7-175  [code=1.20.12   50.10, no name defined]                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhh---hhhhh..hhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------M----------------T--------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------INTERLEUKIN_6  PDB: C:65-9------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1f  PDB: C:7-36           Exon 1.2a  PDB: C:37-72             Exon 1.2c  PDB: C:73-121 UniProt: 105-153        Exon 1.3c  PDB: C:122-175 UniProt: 154-207             Transcript 1
                 1cd9 C   7 ASSLPQSFLLKCLEQVRKIQGDGAALQEKL---CATYKLCHPEELVLLGHSLGIPWAPLSSCPSQALQLAGCLSQLHSGLFLYQGLLQALEGISPELGPTLDTLQLDVADFATTIWQQMEELGMAPALQPTQGAMPAFASAFQRRAGGVLVASHLQSFLEVSYRVLRHLAQP 175
                                    16        26        36   |    43        53        63        73        83        93       103       113       123       133       143       153       163       173  
                                                        36  37                                                                                                                                          

Chain D from PDB  Type:PROTEIN  Length:204
 aligned with CSF3R_MOUSE | P40223 from UniProtKB/Swiss-Prot  Length:837

    Alignment length:212
                                   130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330  
          CSF3R_MOUSE   121 GYPPASPSNLSCLMHLTTNSLVCQWEPGPETHLPTSFILKSFRSRADCQYQGDTIPDCVAKKRQNNCSIPRKNLLLYQYMAIWVQAENMLGSSESPKLCLDPMDVVKLEPPMLQALDIGPDVVSHQPGCLWLSWKPWKPSEYMEQECELRYQPQLKGANWTLVFHLPSSKDQFELCGLHQAPVYTLQMRCIRSSLPGFWSPWSPGLQLRPTM 332
               SCOP domains d1cd9d1 D:2-107 Granulocyte colony-stimulating factor (GC-SF) receptor                                    d1cd9d2 D:1        08-213 Granulocyte colony-stimulating factor (GC-SF) receptor                           SCOP domains
               CATH domains 1cd9D01 D:2-108 Immunoglobulins                                                                            1cd9D02 D:        109-212 Immunoglobulins                                                               - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee....eeeeeee..........eeeeeee.hhhhh....eeeeee.........ee.hhh.....eeeeeeeee..eeee...eeehhhhh......eeee..--------...eeeeeee.hhhhh...eeeeeeeee.......eeeeeee..eeeeeee.......eeeeeeeee.................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----FN3  PDB: D:7-112 UniProt: 126-231                                                                        ----FN3  PDB: D:117-212 UniProt: 236-331                                                            - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cd9 D   2 GYPPASPSNLSCLMHLTTNSLVCQWEPGPETHLPTSFILKSFRSRADCQYQGDTIPDCVAKKRQNNCSIPRKNLLLYQYMAIWVQAENMLGSSESPKLCLDPMDVVKLEPPMLQALD--------QPGCLWLSWKPWKPSEYMEQECELRYQPQLKGANWTLVFHLPSSKDQFELCGLHQAPVYTLQMRCIRSSLPGFWSPWSPGLQLRPTM 213
                                    11        21        31        41        51        61        71        81        91       101       111      |  -     | 131       141       151       161       171       181       191       201       211  
                                                                                                                                              118      127                                                                                      

   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  (2, 6)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CD9)

(-) Gene Ontology  (32, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (CSF3_HUMAN | P09919)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0005130    granulocyte colony-stimulating factor receptor binding    Interacting selectively and non-covalently with the granulocyte colony-stimulating factor receptor.
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
biological process
    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:0071222    cellular response to lipopolysaccharide    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 lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    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:0030851    granulocyte differentiation    The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    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:1901215    negative regulation of neuron death    Any process that stops, prevents or reduces the frequency, rate or extent of neuron death.
    GO:2000251    positive regulation of actin cytoskeleton reorganization    Any process that activates or increases the frequency, rate or extent of actin cytoskeleton reorganization.
    GO:0030838    positive regulation of actin filament polymerization    Any process that activates or increases the frequency, rate or extent of actin polymerization.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0045639    positive regulation of myeloid cell differentiation    Any process that activates or increases the frequency, rate or extent of myeloid cell differentiation.
    GO:0033138    positive regulation of peptidyl-serine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
    GO:0050731    positive regulation of peptidyl-tyrosine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    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:0032092    positive regulation of protein binding    Any process that activates or increases the frequency, rate or extent of protein binding.
    GO:0051897    positive regulation of protein kinase B signaling    Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    GO:0042993    positive regulation of transcription factor import into nucleus    Any process that activates or increases the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus.
    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.
cellular component
    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.

Chain B,D   (CSF3R_MOUSE | P40223)
molecular function
    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: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).
biological process
    GO:0097186    amelogenesis    The process whose specific outcome is the formation of tooth enamel, occurring in two stages: secretory stage and maturation stage.
    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: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:0030593    neutrophil chemotaxis    The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0045637    regulation of myeloid cell differentiation    Any process that modulates the frequency, rate or extent of myeloid cell differentiation.
cellular component
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CSF3R_MOUSE | P402231cto 1gcf 1pgr
        CSF3_HUMAN | P099191gnc 1pgr 1rhg 2d9q

(-) Related Entries Specified in the PDB File

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