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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL KINASE DOMAIN OF MSK1 IN COMPLEX WITH AMP-PNP
 
Authors :  I. D'Angelo, M. Malakhova, Z. Dong
Date :  12 Nov 09  (Deposition) - 21 Apr 10  (Release) - 09 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Kinase, Amp-Pnp, Msk1, Msk, Atp-Binding, Metal-Binding, Nucleotide- Binding, Serine/Threonine-Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Malakhova, I. D'Angelo, H. G. Kim, I. Kurinov, A. M. Bode, Z. Dong
The Crystal Structure Of The Active Form Of The C-Terminal Kinase Domain Of Mitogen- And Stress-Activated Protein Kinase 1.
J. Mol. Biol. V. 399 41 2010
PubMed-ID: 20382163  |  Reference-DOI: 10.1016/J.JMB.2010.03.064

(-) Compounds

Molecule 1 - RIBOSOMAL PROTEIN S6 KINASE ALPHA-5
    ChainsA, B
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainBL21-CODON PLUS (DE3)-RILP
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 414-738
    GeneMSK1, RPS6KA5
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNUCLEAR MITOGEN- AND STRESS-ACTIVATED PROTEIN KINASE 1, 90 KDA RIBOSOMAL PROTEIN S6 KINASE 5, RSK-LIKE PROTEIN KINASE, RSKL

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:66 , LEU A:432 , GLY A:433 , GLU A:434 , GLU A:499 , LEU A:500 , LEU A:501 , GLU A:505 , GLU A:548 , LEU A:551 , ILE A:564 , LYS A:643 , LYS A:716BINDING SITE FOR RESIDUE ANP A 400
2AC2SOFTWAREHOH B:76 , LEU B:432 , GLY B:433 , GLU B:434 , GLU B:499 , LEU B:500 , LEU B:501 , GLU B:505 , GLU B:548 , LEU B:551 , ILE B:564BINDING SITE FOR RESIDUE ANP B 400

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:631 -A:714
2B:631 -B:714

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Ser A:679 -Gly A:680
2Arg A:727 -Glu A:728
3Glu A:728 -Gly A:729
4Val B:670 -Asp B:671
5Asp B:671 -Pro B:672
6Asn B:673 -Lys B:674
7Glu B:728 -Gly B:729

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040634D554NKS6A5_HUMANPolymorphism55911249A/BD554N
2UniProtVAR_040635P574LKS6A5_HUMANPolymorphism34604933A/BP574L
3UniProtVAR_040636Y599CKS6A5_HUMANPolymorphism55968863A/BY599C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040634D554NKS6A5_HUMANPolymorphism55911249AD554N
2UniProtVAR_040635P574LKS6A5_HUMANPolymorphism34604933AP574L
3UniProtVAR_040636Y599CKS6A5_HUMANPolymorphism55968863AY599C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040634D554NKS6A5_HUMANPolymorphism55911249BD554N
2UniProtVAR_040635P574LKS6A5_HUMANPolymorphism34604933BP574L
3UniProtVAR_040636Y599CKS6A5_HUMANPolymorphism55968863BY599C

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KS6A5_HUMAN55-81
432-455
 
  2-
A:432-455
B:432-455
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KS6A5_HUMAN173-185
540-552
 
  2-
A:540-552
B:540-552
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KS6A5_HUMAN55-81
432-455
 
  1-
A:432-455
-
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KS6A5_HUMAN173-185
540-552
 
  1-
A:540-552
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KS6A5_HUMAN55-81
432-455
 
  1-
-
B:432-455
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KS6A5_HUMAN173-185
540-552
 
  1-
-
B:540-552

(-) Exons   (0, 0)

(no "Exon" information available for 3KN5)

(-) 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:282
 aligned with KS6A5_HUMAN | O75582 from UniProtKB/Swiss-Prot  Length:802

    Alignment length:315
                                   424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724     
          KS6A5_HUMAN   415 KDSPFYQHYDLDLKDKPLGEGSFSICRKCVHKKSNQAFAVKIISKRMEANTQKEITALKLCEGHPNIVKLHEVFHDQLHTFLVMELLNGGELFERIKKKKHFSETEASYIMRKLVSAVSHMHDVGVVHRDLKPENLLFTDENDNLEIKIIDFGFARLKPPDNQPLKTPCFTLHYAAPELLNQNGYDESCDLWSLGVILYTMLSGQVPFQSHDRSLTCTSAVEIMKKIKKGDFSFEGEAWKNVSQEAKDLIQGLLTVDPNKRLKMSGLRYNEWLQDGSQLSSNPLMTPDILGSSGAAVHTCVKATFHAFNKYKREG 729
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------------------------------------------3kn5A02              ------------------3kn5A02 A:462-482,A:501-729 Transferase(Phosphotransfe    rase) domain 1                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee.......eee..eeeeeeee.....eeeeeeee..hhhhhhhhhhhhhhh........eeeeee...eeeeeee.....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee..----..eee......ee...----------------------...hhhhhhhhhhhhhhhhhhh.....-------..hhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhh..............hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------N-------------------L------------------------C---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------PROTEIN_KINASE_ATP      ------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kn5 A 415 KDSPFYQHYDLDLKDKPLGEGSFSICRKCVHKKSNQAFAVKIISKRMEANTQKEITALKLCEGHPNIVKLHEVFHDQLHTFLVMELLNGGELFERIKKKKHFSETEASYIMRKLVSAVSHMHDVGVVHRDLKPENLLFTD----LEIKIIDFGFARLKPP----------------------NGYDESCDLWSLGVILYTMLSGQVPFQ-------CTSAVEIMKKIKKGDFSFEGEAWKNVSQEAKDLIQGLLTVDPNKRLKMSGLRYNEWLQDGSQLSSNPLMTPDILGSSGAAVHTCVKATFHAFNKYKREG 729
                                   424       434       444       454       464       474       484       494       504       514       524       534       544       554    |  564       574         -         -  |    604       614        |-      |634       644       654       664       674       684       694       704       714       724     
                                                                                                                                                                     554  559            574                    597                       623     631                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:289
 aligned with KS6A5_HUMAN | O75582 from UniProtKB/Swiss-Prot  Length:802

    Alignment length:315
                                   424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724     
          KS6A5_HUMAN   415 KDSPFYQHYDLDLKDKPLGEGSFSICRKCVHKKSNQAFAVKIISKRMEANTQKEITALKLCEGHPNIVKLHEVFHDQLHTFLVMELLNGGELFERIKKKKHFSETEASYIMRKLVSAVSHMHDVGVVHRDLKPENLLFTDENDNLEIKIIDFGFARLKPPDNQPLKTPCFTLHYAAPELLNQNGYDESCDLWSLGVILYTMLSGQVPFQSHDRSLTCTSAVEIMKKIKKGDFSFEGEAWKNVSQEAKDLIQGLLTVDPNKRLKMSGLRYNEWLQDGSQLSSNPLMTPDILGSSGAAVHTCVKATFHAFNKYKREG 729
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------------------------------------------3kn5B02              ------------------3kn5B02 B:462-482,B:501-729 Transferase(Phosphotransfe    rase) domain 1                                                                                                                                                              CATH domains
           Pfam domains (1) ------------Pkinase-3kn5B01 B:427-687                                                                                                                                                                                                                                            ------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------------Pkinase-3kn5B02 B:427-687                                                                                                                                                                                                                                            ------------------------------------------ Pfam domains (2)
         Sec.struct. author ..hhhhhheee............eeeeeeee....eeeeeeeee..hhhhhhhhhhhhhhh........eeeeee...eeeeeee.....hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee..----..eee......ee...----------------------....hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhh............hhhhhhhhhhhhh.......hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------N-------------------L------------------------C---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------PROTEIN_KINASE_ATP      ------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kn5 B 415 KDSPFYQHYDLDLKDKPLGEGSFSICRKCVHKKSNQAFAVKIISKRMEANTQKEITALKLCEGHPNIVKLHEVFHDQLHTFLVMELLNGGELFERIKKKKHFSETEASYIMRKLVSAVSHMHDVGVVHRDLKPENLLFTD----LEIKIIDFGFARLKPP----------------------NGYDESCDLWSLGVILYTMLSGQVPFQSHDRSLTCTSAVEIMKKIKKGDFSFEGEAWKNVSQEAKDLIQGLLTVDPNKRLKMSGLRYNEWLQDGSQLSSNPLMTPDILGSSGAAVHTCVKATFHAFNKYKREG 729
                                   424       434       444       454       464       474       484       494       504       514       524       534       544       554    |  564       574         -         -  |    604       614       624       634       644       654       664       674       684       694       704       714       724     
                                                                                                                                                                     554  559            574                    597                                                                                                                                    

   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 3KN5)

(-) CATH Domains  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (33, 33)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KS6A5_HUMAN | O75582)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0035175    histone kinase activity (H3-S10 specific)    Catalysis of the transfer of a phosphate group to the serine-10 residue of the N-terminal tail of histone H3.
    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: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: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:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0007173    epidermal growth factor receptor signaling pathway    A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0043990    histone H2A-S1 phosphorylation    The modification of histone H2A by the addition of an phosphate group to a serine residue at position 1 of the histone.
    GO:0043987    histone H3-S10 phosphorylation    The modification of histone H3 by the addition of an phosphate group to a serine residue at position 10 of the histone.
    GO:0043988    histone H3-S28 phosphorylation    The modification of histone H3 by the addition of an phosphate group to a serine residue at position 28 of the histone.
    GO:0016572    histone phosphorylation    The modification of histones by addition of phosphate groups.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0070498    interleukin-1-mediated signaling pathway    A series of molecular signals initiated by the binding of interleukin-1 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    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:0001818    negative regulation of cytokine production    Any process that stops, prevents, or reduces the rate of production of a cytokine.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    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:0032793    positive regulation of CREB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor CREB.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0035066    positive regulation of histone acetylation    Any process that activates or increases the frequency, rate or extent of the addition of an acetyl group to a histone protein.
    GO:0033129    positive regulation of histone phosphorylation    Any process that activates or increases the frequency, rate or extent of the addition of one or more phosphate groups to a histone protein.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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)

UniProtKB/Swiss-Prot
        KS6A5_HUMAN | O755821vzo 3kn6

(-) Related Entries Specified in the PDB File

3kn6 CRYSTAL STRUCTURE OF THE C-TERMINAL KINASE DOMAIN OF MSK1