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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN STE20-LIKE KINASE BOUND TO 4-(4-( 5-CYCLOPROPYL-1H-PYRAZOL-3-YLAMINO)-QUINAZOLIN-2-YLAMINO)-PHENYL)-ACETONITRILE
 
Authors :  A. C. W. Pike, P. Rellos, O. Fedorov, T. Keates, E. Salah, P. Savitsky, E. Papagrigoriou, G. Bunkoczi, J. E. Debreczeni, F. Von Delft, C. H. Arrowsmith, A. Edwards, J. Weigelt, M. Sundstrom, S. Knapp
Date :  08 Mar 07  (Deposition) - 20 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Serine/Threonine-Protein Kinase, Atp-Binding, Phosphorylation, Muscle Development, Kinase, Apoptosis, Germinal Centre Kinase, Serine- Threonine Kinase 2, Nucleotide-Binding, Serine-Threonine-Protein Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. C. W. Pike, P. Rellos, F. H. Niesen, A. Turnbull, A. W. Oliver, S. A. Parker, B. E. Turk, L. H. Pearl, S. Knapp
Activation Segment Dimerization: A Mechanism For Kinase Autophosphorylation Of Non-Consensus Sites.
Embo J. V. 27 704 2008
PubMed-ID: 18239682  |  Reference-DOI: 10.1038/EMBOJ.2008.8

(-) Compounds

Molecule 1 - STE20-LIKE SERINE-THREONINE KINASE
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentKINASE DOMAIN, RESIDUES 19-320
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSTE20-LIKE KINASE, STE20-RELATED SERINE/THREONINE-PROTEIN KINASE, STE20-RELATED KINASE, HSLK, SERINE/THREONINE-PROTEIN KINASE 2, CTCL TUMOR ANTIGEN SE20-9

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2GVD1Ligand/Ion[4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE
3SCN2Ligand/IonTHIOCYANATE ION
4TPO1Mod. Residue
Biological Unit 1 (4, 18)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2GVD2Ligand/Ion[4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE
3SCN4Ligand/IonTHIOCYANATE ION
4TPO2Mod. Residue

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:242 , LEU A:245 , LYS A:249BINDING SITE FOR RESIDUE SCN A1314
2AC2SOFTWARELYS A:63 , VAL A:92 , ILE A:108 , ASP A:173 , GVD A:1316 , HOH A:2024BINDING SITE FOR RESIDUE SCN A1315
3AC3SOFTWAREHIS A:147 , PRO A:211 , TYR A:214 , VAL A:218 , THR A:282 , THR A:283 , EDO A:1311 , HOH A:2144BINDING SITE FOR RESIDUE EDO A1309
4AC4SOFTWAREVAL A:134 , LYS A:137 , GLN A:138 , VAL A:294 , ASP A:295 , SER A:296 , ASN A:297BINDING SITE FOR RESIDUE EDO A1310
5AC5SOFTWAREHIS A:147 , LYS A:150 , ASP A:209 , EDO A:1309BINDING SITE FOR RESIDUE EDO A1311
6AC6SOFTWAREASN A:90 , ASP A:168 , HOH A:2055BINDING SITE FOR RESIDUE EDO A1312
7AC7SOFTWAREASP A:27 , GLN A:133 , PRO A:290BINDING SITE FOR RESIDUE EDO A1313
8AC8SOFTWARELEU A:40 , ALA A:61 , GLU A:109 , CYS A:111 , ALA A:112 , LEU A:162 , SCN A:1315 , HOH A:2148BINDING SITE FOR RESIDUE GVD A1316

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2UV2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2UV2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2UV2)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.SLK_HUMAN40-63  1A:40-63
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.SLK_HUMAN151-163  1A:151-163
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.SLK_HUMAN40-63  2A:40-63
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.SLK_HUMAN151-163  2A:151-163

(-) Exons   (8, 8)

Asymmetric Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003697551ENSE00001319269chr10:105726959-105727653695SLK_HUMAN1-50501A:21-50 (gaps)30
1.2ENST000003697552ENSE00001271743chr10:105750433-105750597165SLK_HUMAN51-105551A:51-10555
1.3ENST000003697553ENSE00000515224chr10:105752356-10575240449SLK_HUMAN106-122171A:106-12217
1.4ENST000003697554ENSE00000515225chr10:105752742-105752891150SLK_HUMAN122-172511A:122-17251
1.5ENST000003697555ENSE00000723471chr10:105758657-10575872973SLK_HUMAN172-196251A:172-19625
1.6ENST000003697556ENSE00000723472chr10:105758877-105759071195SLK_HUMAN196-261661A:196-26166
1.7ENST000003697557ENSE00000723473chr10:105759625-10575970682SLK_HUMAN261-288281A:261-28828
1.8ENST000003697558ENSE00000723474chr10:105761202-105761330129SLK_HUMAN289-331431A:289-30820
1.9ENST000003697559ENSE00000723475chr10:105761930-1057632851356SLK_HUMAN332-7834520--
1.10ENST0000036975510ENSE00000515231chr10:105765319-105765449131SLK_HUMAN784-827440--
1.11ENST0000036975511ENSE00000515232chr10:105765670-105765793124SLK_HUMAN827-868420--
1.12aENST0000036975512aENSE00001271701chr10:105767935-105768114180SLK_HUMAN869-928600--
1.13ENST0000036975513ENSE00000987678chr10:105770574-10577066693SLK_HUMAN929-959310--
1.14ENST0000036975514ENSE00001271696chr10:105777918-105778047130SLK_HUMAN960-1003440--
1.15aENST0000036975515aENSE00001271692chr10:105778542-105778666125SLK_HUMAN1003-1044420--
1.16ENST0000036975516ENSE00000723483chr10:105779492-105779680189SLK_HUMAN1045-1107630--
1.17ENST0000036975517ENSE00001271679chr10:105780246-105780371126SLK_HUMAN1108-1149420--
1.18ENST0000036975518ENSE00001271668chr10:105781378-105781491114SLK_HUMAN1150-1187380--
1.19ENST0000036975519ENSE00001450811chr10:105785332-1057889913660SLK_HUMAN1188-1235480--

(-) 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:286
 aligned with SLK_HUMAN | Q9H2G2 from UniProtKB/Swiss-Prot  Length:1235

    Alignment length:288
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        
            SLK_HUMAN    21 YEHVKRDLNPEDFWEIIGELGDGAFGKVYKAQNKETSVLAAAKVIDTKSEEELEDYMVEIDILASCDHPNIVKLLDAFYYENNLWILIEFCAGGAVDAVMLELERPLTESQIQVVCKQTLDALNYLHDNKIIHRDLKAGNILFTLDGDIKLADFGVSAKNTRTIQRRDSFIGTPYWMAPEVVMCETSKDRPYDYKADVWSLGITLIEMAEIEPPHHELNPMRVLLKIAKSEPPTLAQPSRWSSNFKDFLKKCLEKNVDARWTTSQLLQHPFVTVDSNKPIRELIAEAK 308
               SCOP domains d2uv2a1 A:21-308 STE20  -like serine/threonine-protein kinase, SLK                                                                                                                                                                                                                               SCOP domains
               CATH domains 2uv2A01 A:21-110 Phosp  horylase Kinase; domain 1                                         2uv2A02 A:111-308 Transferase(Phosphotransferase) domain 1                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee..hhhh.eeeeeeee.--.eeeeeeee.....eeeeeeee.....hhhhhhhhhhhhhhh.......eeeeeee..eeeeeee....eehhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......eehhhhhhhhh.........hhhhhh..........hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:21-50 (gaps) Exon 1.2  PDB: A:51-105 UniProt: 51-105                Exon 1.3         -------------------------------------------------Exon 1.5  PDB: A:172-196 ----------------------------------------------------------------Exon 1.7  PDB: A:261-288    Exon 1.8             Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:122-172 UniProt: 122-172          -----------------------Exon 1.6  PDB: A:196-261 UniProt: 196-261                         ----------------------------------------------- Transcript 1 (2)
                 2uv2 A  21 YEHVTRDLNPEDFWEIIGELGD--FGKVYKAQNKETSVLAAAKVIDTKSEEELEDYMVEIDILASCDHPNIVKLLDAFYYENNLWILIEFCAGGAVDAVMLELERPLTESQIQVVCKQTLDALNYLHDNKIIHRDLKAGNILFTLDGDIKLADFGVSAKNTRTIQRRDSFIGTPYWMAPEVVMCETSKDRPYDYKADVWSLGITLIEMAEIEPPHHELNPMRVLLKIAKSEPPTLAQPSRWSSNFKDFLKKCLEKNVDARWTTSQLLQHPFVTVDSNKPIRELIAEAK 308
                                    30        40 |  |   50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        
                                                42 45                                                                                                                                                                                                                                                                       

   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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2UV2)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A   (SLK_HUMAN | Q9H2G2)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0004702    signal transducer, downstream of receptor, with serine/threonine kinase activity    Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: 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:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0031122    cytoplasmic microtubule organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures formed of microtubules and associated proteins in the cytoplasm of a cell.
    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: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:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0030334    regulation of cell migration    Any process that modulates the frequency, rate or extent of cell migration.
    GO:0051893    regulation of focal adhesion assembly    Any process that modulates the frequency, rate or extent of focal adhesion formation, the establishment and maturation of focal adhesions.
    GO:0023014    signal transduction by protein phosphorylation    A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
    GO:0031252    cell leading edge    The area of a motile cell closest to the direction of movement.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SLK_HUMAN | Q9H2G22j51 2jfl 2jfm 4usf

(-) Related Entries Specified in the PDB File

2j51 CRYSTAL STRUCTURE OF HUMAN STE20-LIKE KINASE BOUND TO 5-AMINO-3-((4-(AMINOSULFONYL) PHENYL)AMINO) -N-(2,6-DIFLUOROPHENYL)-1H-1 ,2,4-TRIAZOLE-1-CARBOTHIOAMIDE
2ja0 CRYSTAL STRUCTURE OF HUMAN STE20-LIKE KINASE BOUND TO 4-(4-(5-CYCLOPROPYL-1H-PYRAZOL -3-YLAMINO)-QUINAZOLIN-2-YLAMINO)- BENZONITRILE
2jfl CRYSTAL STRUCTURE OF HUMAN STE20-LIKE KINASE (DIPHOSPHORYLATED FORM) BOUND TO 5- AMINO- 3-((4-(AMINOSULFONYL)PHENYL)AMINO)-N-(2,6 - DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1- CARBOTHIOAMIDE
2jfm CRYSTAL STRUCTURE OF HUMAN STE20-LIKE KINASE (UNLIGANDED FORM)