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(-) Description

Title :  STRUCTURE OF HUMAN SERINE-ARGININE-RICH PROTEIN-SPECIFIC KINASE 2 (SRPK2) BOUND TO PURVALANOL B
 
Authors :  A. C. W. Pike, P. Savitsky, O. Fedorov, T. Krojer, E. Ugochukwu, F. Von D O. Gileadi, A. Edwards, C. H. Arrowsmith, J. Weigelt, C. Bountra, S. Kn
Date :  26 Feb 10  (Deposition) - 14 Apr 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Serine/Threonine-Protein Kinase, Mrna Splicing, Phosphoprotein, Mrna Processing, Differentiation, Nucleotide-Binding, Spliceasome Assembly, Atp Competitive Inhibitor, Kinase, Nucleus, Transferase, Atp-Binding, Splice Factor Trafficking (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. C. W. Pike, P. Savitsky, O. Fedorov, T. Krojer, E. Ugochukwu, F. Von Delft, O. Gileadi, A. Edwards, C. H. Arrowsmith, J. Weigelt, C. Bountra, S. Knapp
Structure Of Human Serine-Arginine-Rich Protein- Specific Kinase 2 (Srpk2) Bound To Purvalanol B
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN SRPK2
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-PRARE2
    FragmentKINASE DOMAIN, RESIDUES 62-267,519-699
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsSYNTHETIC CONSTRUCT ENGINEERED TO REMOVE INTERVENING REGION.
    SynonymSERINE/THREONINE-PROTEIN KINASE SRPK

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO6Ligand/Ion1,2-ETHANEDIOL
3PVB1Ligand/IonPURVALANOL B
4SO47Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:98 , TRP A:100 , GLY A:101 , ALA A:119 , GLU A:178 , LEU A:180 , HIS A:182 , HIS A:183 , LEU A:232 , TYR A:239 , EDO A:1708BINDING SITE FOR RESIDUE PVB A 800
02AC2SOFTWARETYR A:593 , ARG A:632 , ASN A:636 , ARG A:637 , ARG A:642 , HOH A:2027 , HOH A:2105 , HOH A:2106BINDING SITE FOR RESIDUE SO4 A1700
03AC3SOFTWARESER A:687 , GLY A:689 , ARG A:693 , HOH A:2107BINDING SITE FOR RESIDUE SO4 A1701
04AC4SOFTWAREGLY A:101 , HIS A:102 , PHE A:103 , SER A:104BINDING SITE FOR RESIDUE SO4 A1702
05AC5SOFTWAREARG A:559 , ARG A:562 , ARG A:605 , HOH A:2108BINDING SITE FOR RESIDUE SO4 A1703
06AC6SOFTWAREHIS A:598 , SER A:599 , ARG A:605 , ARG A:622BINDING SITE FOR RESIDUE SO4 A1704
07AC7SOFTWAREARG A:622 , HIS A:623BINDING SITE FOR RESIDUE SO4 A1705
08AC8SOFTWAREARG A:605 , ARG A:637 , ARG A:638 , ACT A:1707 , HOH A:2109BINDING SITE FOR RESIDUE SO4 A1706
09AC9SOFTWAREGLN A:560 , ARG A:637 , SO4 A:1706BINDING SITE FOR RESIDUE ACT A1707
10BC1SOFTWAREGLU A:136 , ALA A:540 , ASP A:541 , LEU A:542 , PVB A:800BINDING SITE FOR RESIDUE EDO A1708
11BC2SOFTWAREASP A:150 , ASN A:152 , ASP A:213 , HOH A:2110BINDING SITE FOR RESIDUE EDO A1709
12BC3SOFTWARESER A:166 , SER A:651 , PHE A:653 , THR A:671 , EDO A:1713 , HOH A:2111BINDING SITE FOR RESIDUE EDO A1710
13BC4SOFTWARELEU A:594 , HOH A:2094BINDING SITE FOR RESIDUE EDO A1711
14BC5SOFTWAREPHE A:163 , LYS A:164 , PRO A:649 , TRP A:650 , SER A:651 , ASP A:654 , EDO A:1713BINDING SITE FOR RESIDUE EDO A1712
15BC6SOFTWARELYS A:164 , LEU A:616 , PRO A:649 , EDO A:1710 , EDO A:1712BINDING SITE FOR RESIDUE EDO A1713

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X7G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X7G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041118P515TSRPK2_HUMANPolymorphism56017595AP526T
2UniProtVAR_060390S608NSRPK2_HUMANPolymorphism1050413AS619N
3UniProtVAR_057111L615ISRPK2_HUMANPolymorphism1050418AL626I

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.SRPK2_HUMAN87-110  1A:98-121
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.SRPK2_HUMAN210-222  1A:221-233

(-) Exons   (0, 0)

(no "Exon" information available for 2X7G)

(-) 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:344
 aligned with SRPK2_HUMAN | P78362 from UniProtKB/Swiss-Prot  Length:688

    Alignment length:619
                                    79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679         
          SRPK2_HUMAN    70 PVKIGDLFNGRYHVIRKLGWGHFSTVWLCWDMQGKRFVAMKVVKSAQHYTETALDEIKLLKCVRESDPSDPNKDMVVQLIDDFKISGMNGIHVCMVFEVLGHHLLKWIIKSNYQGLPVRCVKSIIRQVLQGLDYLHSKCKIIHTDIKPENILMCVDDAYVRRMAAEATEWQKAGAPPPSGSAVSTAPQQKPIGKISKNKKKKLKKKQKRQAELLEKRLQEIEELEREAERKIIEENITSAAPSNDQDGEYCPEVKLKTTGLEEAAEAETAKDNGEAEDQEEKEDAEKENIEKDEDDVDQELANIDPTWIESPKTNGHIENGPFSLEQQLDDEDDDEEDCPNPEEYNLDEPNAESDYTYSSSYEQFNGELPNGRHKIPESQFPEFSTSLFSGSLEPVACGSVLSEGSPLTEQEESSPSHDRSRTVSASSTGDLPKAKTRAADLLVNPLDPRNADKIRVKIADLGNACWVHKHFTEDIQTRQYRSIEVLIGAGYSTPADIWSTACMAFELATGDYLFEPHSGEDYSRDEDHIAHIIELLGSIPRHFALSGKYSREFFNRRGELRHITKLKPWSLFDVLVEKYGWPHEDAAQFTDFLIPMLEMVPEKRASAGECLRHPWLNS 688
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2x7gA01 A:81-145,A:157-179 Phosphorylase Kinase; domain 1        2x7gA02    2x7gA01                2x7gA02 A:146-156,A:180-699 Transferase(Phosphotransferase) domain                                                                                                                                                                                                                                                                                    1                                                                                                                                                                                  CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pkinase-2x7gA01 A:526-697                                                                                                                                                   -- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pkinase-2x7gA02 A:526-697                                                                                                                                                   -- Pfam domains (2)
         Sec.struct. author ......ee...eeeeeeeee...eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhhhhhhhh...hhhhhh.....eeeeeee..eeeeeeee.....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..ee....hhh.eee..hhhhhhhhhh.-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------......hhhhh....eee.hhhhhee..........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhh..hhhhhh...hhhhhh...............hhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------------------------------------------------------------------------------N------I------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x7g A  81 PVKIGDLFNGRYHVIRKLGWGHFSTVWLCWDMQGKRFVAMKVVKSAQHYTETALDEIKLLKCVRESDPSDPNKDMVVQLIDDFKISGMNGIHVCMVFEVLGHHLLKWIIKSNYQGLPVRCVKSIIRQVLQGLDYLHSKCKIIHTDIKPENILMCVDDAYVRRMAAE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LLVNPLDPRNADKIRVKIADLGNACWVHKHFTEDIQTRQYRSIEVLIGAGYSTPADIWSTACMAFELATGDYLFEPHSGEDYSRDEDHIAHIIELLGSIPRHFALSGKYSREFFNRRGELRHITKLKPWSLFDVLVEKYGWPHEDAAQFTDFLIPMLEMVPEKRASAGECLRHPWLNS 699
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     |   -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         - |     530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690         
                                                                                                                                                                                               246                                                                                                                                                                                                                                                                                 522                                                                                                                                                                                 

   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 2X7G)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SRPK2_HUMAN | P78362)
molecular function
    GO:0071889    14-3-3 protein binding    Interacting selectively and non-covalently with a 14-3-3 protein. A 14-3-3 protein is any of a large family of approximately 30kDa acidic proteins which exist primarily as homo- and heterodimers within all eukaryotic cells, and have been implicated in the modulation of distinct biological processes by binding to specific phosphorylated sites on diverse target proteins, thereby forcing conformational changes or influencing interactions between their targets and other molecules. Each 14-3-3 protein sequence can be roughly divided into three sections: a divergent amino terminus, the conserved core region and a divergent carboxyl terminus. The conserved middle core region of the 14-3-3s encodes an amphipathic groove that forms the main functional domain, a cradle for interacting with client proteins.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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: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:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    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:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    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:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0045071    negative regulation of viral genome replication    Any process that stops, prevents, or reduces the frequency, rate or extent of viral genome replication.
    GO:0035063    nuclear speck organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of nuclear specks, a class of nuclear body in which splicing factors are localized.
    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:0045787    positive regulation of cell cycle    Any process that activates or increases the rate or extent of progression through the cell cycle.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0043525    positive regulation of neuron apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.
    GO:0045070    positive regulation of viral genome replication    Any process that activates or increases the frequency, rate or extent of viral genome replication.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0048024    regulation of mRNA splicing, via spliceosome    Any process that modulates the frequency, rate or extent of mRNA splicing via a spliceosomal mechanism.
    GO:0000245    spliceosomal complex assembly    The aggregation, arrangement and bonding together of a spliceosomal complex, a ribonucleoprotein apparatus that catalyzes nuclear mRNA splicing via transesterification reactions.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.

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 Related Entries

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

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        SRPK2_HUMAN | P783625myv

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