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(-) Description

Title :  X-RAY STRUCTURE OF SRPK1
 
Authors :  J. C. Ngo, J. Gullingsrud, S. Chakrabarti, B. Nolen, B. E. Aubol, X. D. Fu, J. A. Adams, J. A. Mccammon, G. Ghosh
Date :  26 Oct 04  (Deposition) - 11 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A
Keywords :  Srpk, Kinase, Serine/Threonine-Protein Kinase, Transferase, Alternative Splicing, Atp-Binding, Chromosome Partition, Differentiation, Mrna Processing, Mrna Splicing, Nuclear Protein, Nucleotide-Binding, Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. C. Ngo, J. Gullingsrud, K. Giang, M. J. Yeh, X. D. Fu, J. A. Adams, J. A. Mccammon, G. Ghosh
Sr Protein Kinase 1 Is Resilient To Inactivation.
Structure V. 15 123 2007
PubMed-ID: 17223538  |  Reference-DOI: 10.1016/J.STR.2006.11.011

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE SPRK1
    ChainsA
    EC Number2.7.1.37, 2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentRESIDUES 42-256,474-655
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSRPK1, SRPK1A PROTEIN KINASE, SERINE/ARGININE- RICH PROTEIN SPECIFIC KINASE 1, SR-PROTEIN-SPECIFIC KINASE 1, SFRS PROTEIN KINASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:67 , HIS A:68 , LEU A:69 , GLY A:155 , VAL A:156BINDING SITE FOR RESIDUE EDO A1656
2AC2SOFTWAREASP A:564 , LEU A:568 , GLU A:571BINDING SITE FOR RESIDUE EDO A1657
3AC3SOFTWAREPHE A:542 , TYR A:549 , LEU A:550 , TRP A:606 , LYS A:615 , TYR A:616BINDING SITE FOR RESIDUE EDO A1658
4AC4SOFTWAREGLN A:198 , LEU A:648 , HOH A:2080 , HOH A:2294BINDING SITE FOR RESIDUE EDO A1659
5AC5SOFTWAREHIS A:81 , PHE A:609 , VAL A:613 , GLN A:620BINDING SITE FOR RESIDUE EDO A1660

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WAK)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051669I72TSRPK1_HUMANPolymorphism35519113AI72T

  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.SRPK1_HUMAN86-109  1A:86-109
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.SRPK1_HUMAN209-221  1A:209-221

(-) Exons   (11, 11)

Asymmetric/Biological Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003738251aENSE00002200129chr6:35889119-35888821299SRPK1_HUMAN1-550--
1.1jENST000003738251jENSE00002153471chr6:35888305-3588824561SRPK1_HUMAN5-25210--
1.4cENST000003738254cENSE00002186784chr6:35858790-35858672119SRPK1_HUMAN25-65411A:63-642
1.5ENST000003738255ENSE00002182848chr6:35856700-35856592109SRPK1_HUMAN65-101371A:67-10135
1.6aENST000003738256aENSE00002183727chr6:35855888-3585580188SRPK1_HUMAN101-130301A:101-13030
1.7cENST000003738257cENSE00002191548chr6:35854588-3585450188SRPK1_HUMAN131-160301A:131-16030
1.8bENST000003738258bENSE00002187434chr6:35842116-35842010107SRPK1_HUMAN160-195361A:160-19536
1.9ENST000003738259ENSE00002160762chr6:35840505-35840340166SRPK1_HUMAN196-251561A:196-23641
1.10bENST0000037382510bENSE00002177696chr6:35838736-3583871126SRPK1_HUMAN251-25990--
1.11ENST0000037382511ENSE00002143565chr6:35838271-35838058214SRPK1_HUMAN260-331720--
1.12cENST0000037382512cENSE00002182450chr6:35837678-35837259420SRPK1_HUMAN331-4711410--
1.13cENST0000037382513cENSE00002197474chr6:35836887-35836787101SRPK1_HUMAN471-504341A:475-50430
1.14aENST0000037382514aENSE00002178481chr6:35825145-35825038108SRPK1_HUMAN505-540361A:505-54036
1.15ENST0000037382515ENSE00002194065chr6:35810381-3581031270SRPK1_HUMAN541-564241A:541-56424
1.16cENST0000037382516cENSE00002190158chr6:35806206-3580611493SRPK1_HUMAN564-595321A:564-59532
1.17cENST0000037382517cENSE00002026764chr6:35803265-358007432523SRPK1_HUMAN595-655611A:595-65561

(-) 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:353
 aligned with SRPK1_HUMAN | Q96SB4 from UniProtKB/Swiss-Prot  Length:655

    Alignment length:593
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652   
          SRPK1_HUMAN    63 CKGGYHLVKIGDLFNGRYHVIRKLGWGHFSTVWLSWDIQGKKFVAMKVVKSAEHYTETALDEIRLLKSVRNSDPNDPNREMVVQLLDDFKISGVNGTHICMVFEVLGHHLLKWIIKSNYQGLPLPCVKKIIQQVLQGLDYLHTKCRIIHTDIKPENILLSVNEQYIRRLAAEATEWQRSGAPPPSGSAVSTAPQPKPADKMSKNKKKKLKKKQKRQAELLEKRMQEIEEMEKESGPGQKRPNKQEESESPVERPLKENPPNKMTQEKLEESSTIGQDQTLMERDTEGGAAEINCNGVIEVINYTQNSNNETLRHKEDLHNANDCDVQNLNQESSFLSSQNGDSSTSQETDSCTPITSEVSDTMVCQSSSTVGQSFSEQHISQLQESIRAEIPCEDEQEQEHNGPLDNKGKSTAGNFLVNPLEPKNAEKLKVKIADLGNACWVHKHFTEDIQTRQYRSLEVLIGSGYNTPADIWSTACMAFELATGDYLFEPHSGEEYTRDEDHIALIIELLGKVPRKLIVAGKYSKEFFTKKGDLKHITKLKPWGLFEVLVEKYEWSQEEAAGFTDFLLPMLELIPEKRATAAECLRHPWLNS 655
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1w  akA01 A:63-133,A:145-167 Phosphorylase Kinase; domain 1            1wakA02    1wakA01                1wakA02 A:134-144,A:168-655 Transferase(Phosphotransferase) domain 1                                                                                                                                                                                                                                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pkinase-1wakA01 A:476-653                                                                                                                                                         -- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pkinase-1wakA02 A:476-653                                                                                                                                                         -- Pfam domains (2)
         Sec.struct. author ..--........ee...eeeeeeeee...eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhhhhhhhh...hhhhhh...eeeeeeeee..eeeeeeee.....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..ee....hhh.eee..hhhhhhhhhhhhh----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.........hhhhhhhh.eee.hhhhhee..........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhh..hhhhhhhh.hhhhh................hhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.4-----------------------------------Exon 1.6a  PDB: A:101-130     Exon 1.7c  PDB: A:131-160     ------------------------------------------------------------------------------------------1.10b    Exon 1.11  PDB: - UniProt: 260-331                                      -------------------------------------------------------------------------------------------------------------------------------------------Exon 1.13c  PDB: A:475-504        Exon 1.14a  PDB: A:505-540          Exon 1.15  PDB: A:541-56------------------------------Exon 1.17c  PDB: A:595-655 UniProt: 595-655                   Transcript 1 (1)
           Transcript 1 (2) --Exon 1.5  PDB: A:67-101 [INCOMPLETE] ----------------------------------------------------------Exon 1.8b  PDB: A:160-195           Exon 1.9  PDB: A:196-236 UniProt: 196-251 [INCOMPLETE]  -------------------------------------------------------------------------------Exon 1.12c  PDB: - UniProt: 331-471                                                                                                          --------------------------------------------------------------------------------------------Exon 1.16c  PDB: A:564-595      ------------------------------------------------------------ Transcript 1 (2)
                 1wak A  63 CK--YHLVKIGDLFNGRYHVIRKLGWGHFSTVWLSWDIQGKKFVAMKVVKSAEHYTETALDEIRLLKSVRNSDPNDPNREMVVQLLDDFKISGVNGTHICMVFEVLGHHLLKWIIKSNYQGLPLPCVKKIIQQVLQGLDYLHTKCRIIHTDIKPENILLSVNEQYIRRLAAEAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGNFLVNPLEPKNAEKLKVKIADLGNACWVHKHFTEDIQTRQYRSLEVLIGSGYNTPADIWSTACMAFELATGDYLFEPHSGEEYTRDEDHIALIIELLGKVPRKLIVAGKYSKEFFTKKGDLKHITKLKPWGLFEVLVEKYEWSQEEAAGFTDFLLPMLELIPEKRATAAECLRHPWLNS 655
                             |  |   72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   |     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -  |    482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652   
                             | 67                                                                                                                                                                      236                                                                                                                                                                                                                                            475                                                                                                                                                                                    
                            64                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               

   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 1WAK)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SRPK1_HUMAN | Q96SB4)
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: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: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:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    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: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: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:0050684    regulation of mRNA processing    Any process that modulates the frequency, rate or extent of mRNA processing, those processes involved in the conversion of a primary mRNA transcript into a mature mRNA prior to its translation into polypeptide.
    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:0035092    sperm chromatin condensation    The progressive compaction of the spermatid chromatin so that it reaches a level of condensation that is not compatible with nuclear activities such as transcription or DNA replication.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    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:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SRPK1_HUMAN | Q96SB41wbp 3beg 4wua 5my8

(-) Related Entries Specified in the PDB File

1wbp SRPK1 BOUND TO 9MER DOCKING MOTIF PEPTIDE