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(-) Description

Title :  THREE-DIMENSIONAL THEORETICAL MODEL OF THE LIGAND BINDING DOMAIN OF THE HUMAN B CELL RECPTOR CD40
 
Authors :  J. Bajorath
Date :  26 Mar 96  (Deposition) - 01 Apr 97  (Release) - 01 Apr 97  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Cd40, Receptor, B-Cell, Glycoprotein, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Bajorath, A. Aruffo
Construction And Analysis Of A Detailed Three-Dimensional Model Of The Ligand Binding Domain Of The Human B Cell Receptor Cd40.
Proteins V. 27 59 1997
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - B-CELL SURFACE ANTIGEN CD40
    ChainsA
    FragmentEXTRACELLULAR REGION, RESIDUES 24 - 144
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1CDF)

(-) SS Bonds  (8, 8)

Theoretical Model
No.Residues
1A:26 -A:37
2A:38 -A:51
3A:41 -A:59
4A:62 -A:77
5A:83 -A:103
6A:105 -A:119
7A:111 -A:116
8A:125 -A:143

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Ser A:126 -Pro A:127

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Theoretical Model (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_039301C26QTNR5_HUMANUnclassified  ---AC26Q
2UniProtVAR_039302S35GTNR5_HUMANUnclassified750234130AS35G
3UniProtVAR_077569C37GTNR5_HUMANDisease (HIGM3)  ---AC37G
4UniProtVAR_039303S39TTNR5_HUMANUnclassified  ---AS39T
5UniProtVAR_013628C83RTNR5_HUMANDisease (HIGM3)28931586AC83R
6UniProtVAR_018751S124LTNR5_HUMANPolymorphism11569321AS124L

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

(-) PROSITE Motifs  (2, 4)

Theoretical Model (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TNFR_NGFR_2PS50050 TNFR/NGFR family cysteine-rich region domain profile.TNR5_HUMAN25-59
61-103
104-143
145-186
  3A:25-59
A:61-103
A:104-143
-
2TNFR_NGFR_1PS00652 TNFR/NGFR family cysteine-rich region signature.TNR5_HUMAN26-59  1A:26-59

(-) Exons   (4, 4)

Theoretical Model (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003722851aENSE00001043456chr20:44746911-44747033123TNR5_HUMAN1-17170--
1.2bENST000003722852bENSE00001798746chr20:44750459-4475053779TNR5_HUMAN18-44271A:24-4421
1.3aENST000003722853aENSE00001669431chr20:44750872-44750997126TNR5_HUMAN44-86431A:44-8643
1.4aENST000003722854aENSE00000662548chr20:44751249-44751395147TNR5_HUMAN86-135501A:86-13550
1.4cENST000003722854cENSE00000662549chr20:44751765-4475185894TNR5_HUMAN135-166321A:135-14410
1.5bENST000003722855bENSE00001615165chr20:44755279-4475534062TNR5_HUMAN166-187220--
1.5eENST000003722855eENSE00001731973chr20:44756777-4475686387TNR5_HUMAN187-216300--
1.6aENST000003722856aENSE00001670028chr20:44756969-4475699729TNR5_HUMAN216-225100--
1.6eENST000003722856eENSE00001944254chr20:44757521-44758502982TNR5_HUMAN226-277520--

(-) Sequences/Alignments

Theoretical Model
   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:121
 aligned with TNR5_HUMAN | P25942 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:121
                                    33        43        53        63        73        83        93       103       113       123       133       143 
           TNR5_HUMAN    24 TACREKQYLINSQCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHCHQHKYCDPNLGLRVQQKGTSETDTICTCEEGWHCTSEACESCVLHRSCSPGFGVKQIATGVSDTICE 144
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee....eee.....eeeee........eeee............................eeee........eee.........................eeee........eee Sec.struct. author
                 SAPs(SNPs) --Q--------G-G-T-------------------------------------------R----------------------------------------L-------------------- SAPs(SNPs)
                PROSITE (1) -TNFR_NGFR_2  PDB: A:25-59          -TNFR_NGFR_2  PDB: A:61-103 UniProt: 61-103 TNFR_NGFR_2  PDB: A:104-143             - PROSITE (1)
                PROSITE (2) --TNFR_NGFR_1  PDB: A:26-59         ------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2b            -----------------------------------------Exon 1.4a  PDB: A:86-135 UniProt: 86-135          --------- Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.3a  PDB: A:44-86 UniProt: 44-86     ------------------------------------------------Exon 1.4c  Transcript 1 (2)
                 1cdf A  24 TACREKQYLINSQCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHCHQHKYCDPNLGLRVQQKGTSETDTICTCEEGWHCTSEACESCVLHRSCSPGFGVKQIATGVSDTICE 144
                                    33        43        53        63        73        83        93       103       113       123       133       143 

   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 1CDF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1CDF)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (51, 51)

Theoretical Model(hide GO term definitions)
Chain A   (TNR5_HUMAN | P25942)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0005031    tumor necrosis factor-activated receptor activity    Combining with tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages, to initiate a change in cell function.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0042113    B cell activation    The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
    GO:0042100    B cell proliferation    The expansion of a B cell population by cell division. Follows B cell activation.
    GO:0097190    apoptotic signaling pathway    A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
    GO:0006874    cellular calcium ion homeostasis    Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell.
    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:0071260    cellular response to mechanical 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 mechanical stimulus.
    GO:0042832    defense response to protozoan    Reactions triggered in response to the presence of a protozoan that act to protect the cell or organism.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    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:0002768    immune response-regulating cell surface receptor 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 capable of activating, perpetuating, or inhibiting an immune response.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    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:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0030890    positive regulation of B cell proliferation    Any process that activates or increases the rate or extent of B cell proliferation.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:2000353    positive regulation of endothelial cell apoptotic process    Any process that activates or increases the frequency, rate or extent of endothelial cell apoptotic process.
    GO:0032735    positive regulation of interleukin-12 production    Any process that activates or increases the frequency, rate, or extent of interleukin-12 production.
    GO:0048304    positive regulation of isotype switching to IgG isotypes    Any process that activates or increases the frequency, rate or extent of isotype switching to IgG isotypes.
    GO:0090037    positive regulation of protein kinase C signaling    Any process that increases the frequency, rate, or extent of a series of reactions, mediated by the intracellular serine/threonine kinase protein kinase C, which occurs as a result of a single trigger reaction or compound.
    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:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0043491    protein kinase B signaling    A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase B (also called AKT), which occurs as a result of a single trigger reaction or compound.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0051023    regulation of immunoglobulin secretion    Any process that modulates the frequency, rate or extent of the regulated release of immunoglobulins from a cell.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (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:0033209    tumor necrosis factor-mediated signaling pathway    A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0035631    CD40 receptor complex    A protein complex that contains at least CD40 (a cell surface receptor of the tumour necrosis factor receptor (TNFR) superfamily), and other signaling molecules.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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: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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    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
        TNR5_HUMAN | P259421czz 1d00 1fll 1lb6 3qd6 5dmi 5dmj 5ihl

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