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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF JAML AND COXSACKIE AND ADENOVIRUS RECEPTOR, CAR
 
Authors :  P. Verdino, I. A. Wilson
Date :  12 Apr 10  (Deposition) - 22 Sep 10  (Release) - 22 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Immunoglobulin Tandem Domain, Immune Receptor Complex, Cell Adhesion, Cell Junction, Glycoprotein, Immunoglobulin Domain, Membrane, Transmembrane, Costimulation, Phosphoprotein, Receptor, Secreted, Tight Junction, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Verdino, D. A. Witherden, W. L. Havran, I. A. Wilson
The Molecular Interaction Of Car And Jaml Recruits The Central Cell Signal Transducer Pi3K.
Science V. 329 1210 2010
PubMed-ID: 20813955  |  Reference-DOI: 10.1126/SCIENCE.1187996
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - JUNCTIONAL ADHESION MOLECULE-LIKE
    ChainsA
    EngineeredYES
    Expression SystemDROSOPHILA MELANOGASTER
    Expression System CommonFRUIT FLY
    Expression System PlasmidPMT/BIP/V5-HIS A
    Expression System Taxid7227
    Expression System Vector TypePLASMID
    FragmentEXTRACELLULAR DOMAIN (UNP RESIDUES 21-280)
    GeneAMICA1, GM638, JAML
    MutationYES
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymDENDRITIC CELL-SPECIFIC PROTEIN CREA7, MCREA7
 
Molecule 2 - COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR HOMOLOG
    ChainsB
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPBAC6
    Expression System Taxid7108
    Expression System Vector TypePLASMID
    FragmentEXTRACELLULAR DOMAIN (UNP RESIDUES 18-236)
    GeneCAR, CXADR
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymCAR, MCAR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2FUC1Ligand/IonALPHA-L-FUCOSE
3MAN1Ligand/IonALPHA-D-MANNOSE
4NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:65 , ASN A:69 , NAG A:402 , FUC A:406BINDING SITE FOR RESIDUE NAG A 401
2AC2SOFTWARENAG A:401 , BMA A:403 , FUC A:406BINDING SITE FOR RESIDUE NAG A 402
3AC3SOFTWAREGLU A:121 , NAG A:402 , MAN A:405BINDING SITE FOR RESIDUE BMA A 403
4AC4SOFTWAREGLY A:18 , BMA A:403BINDING SITE FOR RESIDUE MAN A 405
5AC5SOFTWARENAG A:401 , NAG A:402BINDING SITE FOR RESIDUE FUC A 406
6AC6SOFTWAREASN A:105BINDING SITE FOR RESIDUE NAG A 501
7AC7SOFTWAREARG A:185 , THR B:75 , ASN B:87 , NAG B:302BINDING SITE FOR RESIDUE NAG B 301
8AC8SOFTWARENAG B:301BINDING SITE FOR RESIDUE NAG B 302

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:25 -A:99
2A:138 -A:216
3B:22 -B:101
4B:127 -B:204
5B:143 -B:193

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala B:106 -Pro B:107
2Lys B:146 -Glu B:147
3Leu B:150 -Pro B:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MJ7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MJ7)

(-) Exons   (0, 0)

(no "Exon" information available for 3MJ7)

(-) 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:229
 aligned with JAML_MOUSE | Q80UL9 from UniProtKB/Swiss-Prot  Length:379

    Alignment length:229
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250         
           JAML_MOUSE    31 PQLRVHVGESVLMGCVVQRTEEKHVDRVDWLFSKDKDDASEYVLFYYSNLSVPTGRFQNRSHLVGDTFHNDGSLLLQDVQKADEGIYTCEIRLKNESMVMKKPVELWVLPEEPKDLRVRVGDTTQMRCSIQSTEEKRVTKVNWMFSSGSHTEEETVLSYDSNMRSGKFQSLGRFRNRVDLTGDISRNDGSIKLQTVKESDQGIYTCSIYVGKLESRKTIVLHVVQDEFQ 259
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....eee...........eeeeeeeee.......eeeeeee..eeee.hhhh..eee..........eee...hhhhheeeeeeeee....eeeeeeeeeeee.....eeeee....eee....ee.......eeeeeee.......eeeeeee.......ee........eee..hhhhh...eee...hhhhheeeeeeeee..eeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mj7 A  11 PQLRVHVGESVLMGCVVQRTEEKHVDRVDWLFSKDKDDASEYVLFYYSNLSVPTGRFQNRSHLVGDTFHNDGSLLLQDVQKADEGIYTCEIRLKNESMVMKKPVELWVLPEEPRDLRVRVGDTTQMRCSIQSTEEKRVTKVNWMFSSGSHTEEETVLSYDSNMRSGKFQSLGRFRNRVDLTGDISRNDGSIKLQTVKESDQGIYTCSIYVGKLESRKTIVLHVVQDEFQ 239
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230         

Chain B from PDB  Type:PROTEIN  Length:189
 aligned with CXAR_MOUSE | P97792 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:208
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        
           CXAR_MOUSE    22 ITTPEQRIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPSDNQIVDQVIILYSGDKIYDNYYPDLKGRVHFTSNDVKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKFLLTVLVKPSGTRCFVDGSEEIGNDFKLKCEPKEGSLPLQFEWQKLSDSQTMPTPWLAEMTSPVISVKNASSEYSGTYSCTVQNRVGSDQCMLRLDV 229
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------Ig_2-3mj7B01      B:118-210                                                                   Pfam domains (1)
           Pfam domains (2) V-set-3mj7B02 B:3-127                                                                                                        ----------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....eeeeee....eee..............eeeeeeee.....eeeeeeeee..eee...hhhhh..eee...hhhhh...eee...hhhh.eeeeeeeee..eeeeeeeeeeee......eeee.-----.....eeee........eeeee.------.hhhhhhhh...ee....--------.eeeee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mj7 B   3 ITTPEQRIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPSDNQIVDQVIILYSGDKIYDNYYPDLKGRVHFTSNDVKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKFLLTVLVKPSGTRCFVD-----GNDFKLKCEPKEGSLPLQFEWQK------MPTPWLAEMTSPVISVKN--------YSCTVQNRVGSDQCMLRLDV 210
                                    12        22        32        42        52        62        72        82        92       102       112       122       | -   |   142       152     |   -  |    172       182       192       202        
                                                                                                                                                         130   136                   158    165              182      191                   

   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 3MJ7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MJ7)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)

(-) Gene Ontology  (58, 70)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (JAML_MOUSE | Q80UL9)
molecular function
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    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:0046629    gamma-delta T cell activation    The change in morphology and behavior of a gamma-delta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
    GO:0007157    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules    The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
    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:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0035696    monocyte extravasation    The migration of a monocyte from the blood vessels into the surrounding tissue.
    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:0072672    neutrophil extravasation    The migration of a neutrophil from the blood vessels into the surrounding tissue.
    GO:0060054    positive regulation of epithelial cell proliferation involved in wound healing    Any process that activates or increases the rate or extent of epithelial cell proliferation, contributing to the restoration of integrity to a damaged tissue following an injury.
cellular component
    GO:0005923    bicellular tight junction    An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
    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: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.
    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.

Chain B   (CXAR_MOUSE | P97792)
molecular function
    GO:0030165    PDZ domain binding    Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
    GO:0008013    beta-catenin binding    Interacting selectively and non-covalently with the beta subunit of the catenin complex.
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0086082    cell adhesive protein binding involved in AV node cell-bundle of His cell communication    Interacting selectively and non-covalently with any protein or protein complex that results in the connection of an AV node cell with a bundle of His cell and contributes to the communication between the two cells.
    GO:0071253    connexin binding    Interacting selectively and non-covalently with a connexin, any of a group of related proteins that assemble to form gap junctions.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    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: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.
biological process
    GO:0086067    AV node cell to bundle of His cell communication    The process that mediates interactions between an AV node cell and its surroundings that contributes to the process of the AV node cell communicating with a bundle of His cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
    GO:0086072    AV node cell-bundle of His cell adhesion involved in cell communication    The attachment of an AV node cell to an bundle of His cell via adhesion molecules that results in the cells being juxtaposed so that they can communicate.
    GO:0031532    actin cytoskeleton reorganization    A process that is carried out at the cellular level which results in dynamic structural changes to the arrangement of constituent parts of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0048739    cardiac muscle fiber development    The process whose specific outcome is the progression of cardiac muscle fiber over time, from its formation to the mature structure.
    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:0045216    cell-cell junction organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell-cell junction. A cell-cell junction is a specialized region of connection between two cells.
    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:0010669    epithelial structure maintenance    A tissue homeostatic process required for the maintenance of epithelial structure.
    GO:0046629    gamma-delta T cell activation    The change in morphology and behavior of a gamma-delta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
    GO:0008354    germ cell migration    The orderly movement of a cell specialized to produce haploid gametes through the embryo from its site of production to the place where the gonads will form.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0007157    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules    The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
    GO:0034109    homotypic cell-cell adhesion    The attachment of a cell to a second cell of the identical type via adhesion molecules.
    GO:0007005    mitochondrion organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
    GO:0060044    negative regulation of cardiac muscle cell proliferation    Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle cell proliferation.
    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:0060054    positive regulation of epithelial cell proliferation involved in wound healing    Any process that activates or increases the rate or extent of epithelial cell proliferation, contributing to the restoration of integrity to a damaged tissue following an injury.
    GO:0098904    regulation of AV node cell action potential    Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in an atrioventricular node myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
    GO:0016337    single organismal cell-cell adhesion    The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
    GO:0070633    transepithelial transport    The directed movement of a substance from one side of an epithelium to the other.
cellular component
    GO:0001669    acrosomal vesicle    A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome.
    GO:0005912    adherens junction    A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
    GO:0016327    apicolateral plasma membrane    The apical end of the lateral plasma membrane of epithelial cells.
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0005923    bicellular tight junction    An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
    GO:0044297    cell body    The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
    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:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0030175    filopodium    Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    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:0014704    intercalated disc    A complex cell-cell junction at which myofibrils terminate in cardiomyocytes; mediates mechanical and electrochemical integration between individual cardiomyocytes. The intercalated disc contains regions of tight mechanical attachment (fasciae adherentes and desmosomes) and electrical coupling (gap junctions) between adjacent cells.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0031594    neuromuscular junction    The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CXAR_MOUSE | P977923jz7
        JAML_MOUSE | Q80UL93mj6 3mj9

(-) Related Entries Specified in the PDB File

3mj6 3mj8 3mj9