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(-) Description

Title :  CRYSTAL STRUCTURE OF THE KINASE DOMAIN OF TRAF2 AND NCK-INTERACTING PROTEIN KINASE WITH NCB-0846
 
Authors :  N. Ohbayashi, M. Kukimoto-Niino, T. Yamada, M. Shirouzu
Date :  13 Aug 15  (Deposition) - 17 Aug 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Masuda, Y. Uno, N. Ohbayashi, H. Ohata, A. Mimata, M. Kukimoto-Niino, H. Moriyama, S. Kashimoto, T. Inoue, N. Goto, K. Okamoto, M. Shirouzu, M. Sawa, T. Yamada
Tnik Inhibition Abrogates Colorectal Cancer Stemness
Nat Commun V. 7 12586 2016
PubMed-ID: 27562646  |  Reference-DOI: 10.1038/NCOMMS12586

(-) Compounds

Molecule 1 - TRAF2 AND NCK-INTERACTING PROTEIN KINASE
    ChainsA, B, C
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemBACULOVIRUS EXPRESSION VECTOR PFASTBAC1-HM
    Expression System Taxid274590
    GeneTNIK, KIAA0551
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
158C3Ligand/IonCIS-4-{[2-(1H-BENZIMIDAZOL-5-YLAMINO)QUINAZOLIN-8-YL]OXY}CYCLOHEXANOL
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
158C1Ligand/IonCIS-4-{[2-(1H-BENZIMIDAZOL-5-YLAMINO)QUINAZOLIN-8-YL]OXY}CYCLOHEXANOL
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
158C1Ligand/IonCIS-4-{[2-(1H-BENZIMIDAZOL-5-YLAMINO)QUINAZOLIN-8-YL]OXY}CYCLOHEXANOL
2SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
158C1Ligand/IonCIS-4-{[2-(1H-BENZIMIDAZOL-5-YLAMINO)QUINAZOLIN-8-YL]OXY}CYCLOHEXANOL
2SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:31 , ASN A:33 , VAL A:39 , ALA A:52 , MET A:105 , GLU A:106 , CYS A:108 , GLY A:111 , SER A:112 , ASP A:115 , GLN A:157 , LEU A:160 , VAL A:170binding site for residue 58C A 401
2AC2SOFTWAREARG A:19 , ASP B:211 , LYS B:213 , HIS B:274 , SER B:275binding site for residue SO4 A 402
3AC3SOFTWAREVAL B:31 , VAL B:39 , ALA B:52 , MET B:105 , GLU B:106 , PHE B:107 , CYS B:108 , GLY B:111 , ASP B:115 , GLN B:157 , LEU B:160 , VAL B:170binding site for residue 58C B 401
4AC4SOFTWAREVAL C:31 , ALA C:52 , MET C:105 , GLU C:106 , CYS C:108 , GLY C:111 , ASP C:115 , GLN C:157 , LEU C:160 , VAL C:170 , ASP C:171binding site for residue 58C C 401
5AC5SOFTWAREARG B:19 , ASP C:211 , LYS C:213 , HIS C:274 , SER C:275binding site for residue SO4 C 402
6AC6SOFTWARELYS A:213 , HIS A:274 , SER A:275 , ARG C:19binding site for residue SO4 C 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D7A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D7A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D7A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D7A)

(-) Exons   (0, 0)

(no "Exon" information available for 5D7A)

(-) 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:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh......eeeeeeeeee..eeeeeeee.....eeeeeeeee..hhhhhhhhhhhhhhhhh.......eeeeeee.......eeeeeee......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...........eee.....eee...............hhhhh..........hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7a A  11 DEIDLSALRDPAGIFELVELVGNGTYGQVYKGRHVKTGQLAAIKVMDVTGDEEEEIKQEINMLKKYSHHRNIATYYGAFIKKNPPGMDDQLWLVMEFCGAGSVTDLIKNTKGNTLKEEWIAYICREILRGLSHLHQHKVIHRDIKGQNVLLTENAEVKLVDFGVNTFIGTPYWMAPEVIACDENPDATYDFKSDLWSLGITAIEMAEGAPPLCDMHPMRALFLIPRNPAPRLKSKKWSKKFQSFIESCLVKNHSQRPATEQLMKHPFIRDQPNERQVRIQLKDHIDRTK 310
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   ||  191       201       211       221       231       241       251       261       271       281       291       301         
                                                                                                                                                                                             174|                                                                                                                            
                                                                                                                                                                                              186                                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:286
                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh......eeeeeeeeee..eeeeeeee.....eeeeeeeeehhhhhhhhhhhhhhhhhhh.......eeeeeee.......eeeeeee......hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh...........eee.....eee..............................hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh..........hhhhhhhhhhhh........hhhhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7a B  11 DEIDLSALRDPAGIFELVELVGNGTYGQVYKGRHVKTGQLAAIKVMDVTGDEEEEIKQEINMLKKYSHHRNIATYYGAFIKKNPPGMDDQLWLVMEFCGAGSVTDLIKNTKGNTLKEEWIAYICREILRGLSHLHQHKVIHRDIKGQNVLLTENAEVKLVDFGVNTFIGTPYWMAPEVIACDENPDATYDFKSDLWSLGITAIEMAEGAPPLCDMHPMRALFLIPRNPAPRLKSKKWSKKFQSFIESCLVKNHSQRPATEQLMKHPFIRDQPNERQVRIQLKDHID 307
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   ||  191       201       211       221       231       241       251       261       271       281       291       301      
                                                                                                                                                                                             174|                                                                                                                         
                                                                                                                                                                                              186                                                                                                                         

Chain C from PDB  Type:PROTEIN  Length:286
                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeee.....eeeeeee.....eeeeeeeee...hhhhhhhhhhhhhhhh.......eeeeeee.......eeeeeee.....eehhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.............................hhhhhhhhhhhhhhhhhhh.......hhhhhhhhh.............hhhhhhhhhhhh........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7a C  13 IDLSALRDPAGIFELVELVGNGTYGQVYKGRHVKTGQLAAIKVMDVTGDEEEEIKQEINMLKKYSHHRNIATYYGAFIKKNPPGMDDQLWLVMEFCGAGSVTDLIKNTKGNTLKEEWIAYICREILRGLSHLHQHKVIHRDIKGQNVLLTENAEVKLVDFGNTFIGTPYWMAPEVIACDENPDATYDFKSDLWSLGITAIEMAEGAPPLCDMHPMRALFLIPRNPAPRLKSKKWSKKFQSFIESCLVKNHSQRPATEQLMKHPFIRDQPNERQVRIQLKDHIDRTK 310
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172||     194       204       214       224       234       244       254       264       274       284       294       304      
                                                                                                                                                                                          173|                                                                                                                            
                                                                                                                                                                                           186                                                                                                                            

   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 5D7A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D7A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D7A)

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        TNIK_HUMAN | Q9UKE52x7f 5ax9 5cwz

(-) Related Entries Specified in the PDB File

5ax9 5cwz