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(-) Description

Title :  CRYSTAL STRUCTURE OF A KINASE MARK2/PAR-1 MUTANT
 
Authors :  S. Panneerselvam, A. Marx, E. -M. Mandelkow, E. Mandelkow
Date :  20 Aug 07  (Deposition) - 26 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Serine/Threonine Protein Kinase; Mark; Par-1; Kin1; Uba Domain, Signaling Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Panneerselvam, A. Marx, E. -M. Mandelkow, E. Mandelkow
Crystal Structure Of A Kinase Mark2/Par-1 Mutant
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE MARK2
    ChainsA, B
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDEST17
    Expression System StrainBL21AI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCATALYTIC AND UBIQUITIN-ASSOCIATED DOMAINS
    GeneMARK2
    MutationYES
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymMAP/MICROTUBULE AFFINITY-REGULATING KINASE 2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2R0I)

(-) Sites  (0, 0)

(no "Site" information available for 2R0I)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R0I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R0I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R0I)

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.MARK2_RAT59-82
 
  2A:59-82
B:59-82
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MARK2_RAT171-183
 
  2A:171-183
B:171-183
3UBAPS50030 Ubiquitin-associated domain (UBA) profile.MARK2_RAT323-362
 
  2A:323-362
B:323-362
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.MARK2_RAT59-82
 
  1A:59-82
-
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MARK2_RAT171-183
 
  1A:171-183
-
3UBAPS50030 Ubiquitin-associated domain (UBA) profile.MARK2_RAT323-362
 
  1A:323-362
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.MARK2_RAT59-82
 
  1-
B:59-82
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MARK2_RAT171-183
 
  1-
B:171-183
3UBAPS50030 Ubiquitin-associated domain (UBA) profile.MARK2_RAT323-362
 
  1-
B:323-362

(-) Exons   (10, 20)

Asymmetric Unit (10, 20)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000287631ENSRNOE00000431295chr1:210022099-21002201981MARK2_RAT1-18180--
1.2ENSRNOT000000287632ENSRNOE00000442142chr1:209972642-209972463180MARK2_RAT19-78602A:48-78
B:48-78
31
31
1.3ENSRNOT000000287633ENSRNOE00000206780chr1:209972235-20997218254MARK2_RAT79-96182A:79-96
B:79-96
18
18
1.4ENSRNOT000000287634ENSRNOE00000206781chr1:209969442-20996939449MARK2_RAT97-113172A:97-113
B:97-113
17
17
1.5ENSRNOT000000287635ENSRNOE00000206782chr1:209969130-20996906566MARK2_RAT113-135232A:113-135
B:113-135
23
23
1.6ENSRNOT000000287636ENSRNOE00000206783chr1:209968946-20996887671MARK2_RAT135-158242A:135-158
B:135-158
24
24
1.7ENSRNOT000000287637ENSRNOE00000206784chr1:209968661-20996860557MARK2_RAT159-177192A:159-177
B:159-177
19
19
1.8ENSRNOT000000287638ENSRNOE00000206785chr1:209967997-209967761237MARK2_RAT178-256792A:178-256 (gaps)
B:178-256 (gaps)
79
79
1.9ENSRNOT000000287639ENSRNOE00000206786chr1:209967144-209967025120MARK2_RAT257-296402A:257-296
B:257-296
40
40
1.10bENSRNOT0000002876310bENSRNOE00000206787chr1:209966915-209966816100MARK2_RAT297-330342A:297-330
B:297-330
34
34
1.11bENSRNOT0000002876311bENSRNOE00000206788chr1:209966731-209966619113MARK2_RAT330-367382A:330-363
B:330-363
34
34
1.12ENSRNOT0000002876312ENSRNOE00000206789chr1:209965747-209965615133MARK2_RAT368-412450--
1.13ENSRNOT0000002876313ENSRNOE00000206790chr1:209965379-209965207173MARK2_RAT412-469580--
1.14ENSRNOT0000002876314ENSRNOE00000206791chr1:209964998-20996490198MARK2_RAT470-502330--
1.16ENSRNOT0000002876316ENSRNOE00000206792chr1:209963423-209963166258MARK2_RAT502-588870--
1.17ENSRNOT0000002876317ENSRNOE00000369651chr1:209962194-20996216827MARK2_RAT588-597100--
1.18ENSRNOT0000002876318ENSRNOE00000206793chr1:209960262-20996021845MARK2_RAT597-612160--
1.19ENSRNOT0000002876319ENSRNOE00000206800chr1:209959623-209958925699MARK2_RAT612-7311200--

(-) 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:300
 aligned with MARK2_RAT | O08679 from UniProtKB/Swiss-Prot  Length:722

    Alignment length:316
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357      
            MARK2_RAT    48 PHIGNYRLLKTIGKGNFAKVKLARHILTGKEVAVKIIDKTQLNSSSLQKLFREVRIMKVLNHPNIVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSAVQYCHQKFIVHRDLKAENLLLDADMNIKIADFGFSNEFTFGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKKFLILNPSKRGTLEQIMKDRWMNVGHEDDELKPYVEPLPDYKDPRRTELMVSMGYTREEIQDSLVGQRYNEVMATYLLLGY 363
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------2r0iA02 A:132-321 Transferase(Phosphotransferase) domain 1                                                                                                                                    2r0iA03 A:322-363                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..eeeeeeeee...eeeeeeee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhh.......eeeeee...eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee...----------------.hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh.hhhhhh.hhhhhh..................hhhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------PROTEIN_KINASE_ATP      ----------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------------------UBA  PDB: A:323-362 UniProt: 323-362    - PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:48-78         Exon 1.3          Exon 1.4         ---------------------Exon 1.6  PDB: A:135-158Exon 1.7           Exon 1.8  PDB: A:178-256 (gaps) UniProt: 178-256                               Exon 1.9  PDB: A:257-296                Exon 1.10b  PDB: A:297-330        --------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------Exon 1.5  PDB: A:113-13--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.11b  PDB: A:330-363         Transcript 1 (2)
                 2r0i A  48 PHIGNYRLLKTIGKGNFAKVKLARHILTGKEVAVKIIDKTQLNSSSLQKLFREVRIMKVLNHPNIVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSAVQYCHQKFIVHRDLKAENLLLDADMNIKIADF----------------GSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKKFLILNPSKRGTLEQIMKDRWMNVGHEDDELKPYVAPLPDYKDPRRTELMVSMGYTREEIQDSLVGQRYNEVMATYLLLGY 363
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187      |  -         -   |   217       227       237       247       257       267       277       287       297       307       317       327       337       347       357      
                                                                                                                                                                            194              211                                                                                                                                                        

Chain B from PDB  Type:PROTEIN  Length:300
 aligned with MARK2_RAT | O08679 from UniProtKB/Swiss-Prot  Length:722

    Alignment length:316
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357      
            MARK2_RAT    48 PHIGNYRLLKTIGKGNFAKVKLARHILTGKEVAVKIIDKTQLNSSSLQKLFREVRIMKVLNHPNIVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSAVQYCHQKFIVHRDLKAENLLLDADMNIKIADFGFSNEFTFGNKLDTFCGSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKKFLILNPSKRGTLEQIMKDRWMNVGHEDDELKPYVEPLPDYKDPRRTELMVSMGYTREEIQDSLVGQRYNEVMATYLLLGY 363
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------2r0iB02 B:132-321 Transferase(Phosphotransferase) domain 1                                                                                                                                    2r0iB03 B:322-363                          CATH domains
           Pfam domains (1) -----Pkinase-2r0iB01 B:53-304                                                                                                                                                                                                                                    ----------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----Pkinase-2r0iB02 B:53-304                                                                                                                                                                                                                                    ----------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .ee..eeeeeeeee...eeeeeeee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhh.......eeeeee...eeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee...----------------.hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh..................hhhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------PROTEIN_KINASE_ATP      ----------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------------------UBA  PDB: B:323-362 UniProt: 323-362    - PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:48-78         Exon 1.3          Exon 1.4         ---------------------Exon 1.6  PDB: B:135-158Exon 1.7           Exon 1.8  PDB: B:178-256 (gaps) UniProt: 178-256                               Exon 1.9  PDB: B:257-296                Exon 1.10b  PDB: B:297-330        --------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------Exon 1.5  PDB: B:113-13--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.11b  PDB: B:330-363         Transcript 1 (2)
                 2r0i B  48 PHIGNYRLLKTIGKGNFAKVKLARHILTGKEVAVKIIDKTQLNSSSLQKLFREVRIMKVLNHPNIVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSAVQYCHQKFIVHRDLKAENLLLDADMNIKIADF----------------GSPPYAAPELFQGKKYDGPEVDVWSLGVILYTLVSGSLPFDGQNLKELRERVLRGKYRIPFYMSTDCENLLKKFLILNPSKRGTLEQIMKDRWMNVGHEDDELKPYVAPLPDYKDPRRTELMVSMGYTREEIQDSLVGQRYNEVMATYLLLGY 363
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187      |  -         -   |   217       227       237       247       257       267       277       287       297       307       317       327       337       347       357      
                                                                                                                                                                            194              211                                                                                                                                                        

   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 2R0I)

(-) CATH Domains  (2, 4)

Asymmetric Unit

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MARK2_RAT | O08679)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0050321    tau-protein kinase activity    Catalysis of the reaction: ATP + tau-protein = ADP + O-phospho-tau-protein.
    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.
biological process
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    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:0030010    establishment of cell polarity    The specification and formation of anisotropic intracellular organization or cell growth patterns.
    GO:0045197    establishment or maintenance of epithelial cell apical/basal polarity    Any cellular process that results in the specification, formation or maintenance of the apicobasal polarity of an epithelial cell.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    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:0001764    neuron migration    The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature.
    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:0010976    positive regulation of neuron projection development    Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    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:0050770    regulation of axonogenesis    Any process that modulates the frequency, rate or extent of axonogenesis, the generation of an axon, the long process of a neuron.
    GO:0051493    regulation of cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures.
cellular component
    GO:0005884    actin filament    A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0016328    lateral plasma membrane    The portion of the plasma membrane at the lateral side of the cell. In epithelial cells, lateral plasma membranes are on the sides of cells which lie at the interface of adjacent cells.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0097427    microtubule bundle    An arrangement of closely apposed microtubules running parallel to each other.
    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
        MARK2_RAT | O086791y8g 1zmu 1zmv 1zmw 2wzj

(-) Related Entries Specified in the PDB File

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