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(-) Description

Title :  MONOCLINIC COMPLEX STRUCTURE OF HUMAN PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA') WITH THE INHIBITOR 4'-CARBOXY-6,8-CHLORO-FLAVONOL (FLC21)
 
Authors :  K. Niefind, N. Bischoff, S. M. Yarmoluk, V. G. Bdzhola, A. G. Golub, A. O. A. O. Prykhod'Ko
Date :  20 Oct 16  (Deposition) - 18 Jan 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein Kinase Ck2, Casein Kinase 2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Niefind, N. Bischoff, A. G. Golub, V. G. Bdzhola, A. O. Balanda, A. O. Prykhod'Ko, S. M. Yarmoluk
Structural Hypervariability Of The Two Human Protein Kinase Ck2 Catalytic Subunit Paralogs Revealed By Complex Structures With A Flavonol- And A Thieno[2, 3-D]Pyrimidine-Based Inhibitor.
Pharmaceuticals V. 10 2017
PubMed-ID: 28085026  |  Reference-DOI: 10.3390/PH10010009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CASEIN KINASE II SUBUNIT ALPHA'
    Chains: A, B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CSNK2A2, CK2A2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CK II ALPHA'

 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  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
17FC2Ligand/Ion4-[6,8-BIS(CHLORANYL)-3-OXIDANYL-4-OXIDANYLIDENE-CHROMEN-2-YL]BENZOIC ACID
2CL2Ligand/IonCHLORIDE ION
3GOL4Ligand/IonGLYCEROL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
17FC1Ligand/Ion4-[6,8-BIS(CHLORANYL)-3-OXIDANYL-4-OXIDANYLIDENE-CHROMEN-2-YL]BENZOIC ACID
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
17FC1Ligand/Ion4-[6,8-BIS(CHLORANYL)-3-OXIDANYL-4-OXIDANYLIDENE-CHROMEN-2-YL]BENZOIC ACID
2CL-1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:67 , LYS A:69 , ILE A:96 , PHE A:114 , GLU A:115 , TYR A:116 , ILE A:117 , MET A:164 , ILE A:175 , ASP A:176 , HOH A:529 , ARG B:44binding site for residue 7FC A 401
2AC2SOFTWAREGLN A:124 , GLN A:127 , LEU B:42 , GLU B:53 , PHE B:55 , ILE B:70 , HOH B:655binding site for residue GOL A 402
3AC3SOFTWARESER A:278 , ARG A:279 , SER B:278 , ARG B:279binding site for residue CL A 403
4AC4SOFTWAREARG A:44 , GLY B:47 , ARG B:48 , VAL B:67 , LYS B:69 , ILE B:96 , PHE B:114 , GLU B:115 , TYR B:116 , ILE B:117 , MET B:164 , ILE B:175 , ASP B:176 , GOL B:403 , HOH B:508 , HOH B:584binding site for residue 7FC B 401
5AC5SOFTWARELYS B:123 , PHE B:198 , GLU B:231 , HOH B:569binding site for residue GOL B 402
6AC6SOFTWAREGLY B:47 , ARG B:48 , ASN B:119 , ASP B:121 , PHE B:122 , PRO B:160 , HIS B:161 , 7FC B:401 , HOH B:646binding site for residue GOL B 403
7AC7SOFTWAREPRO B:32 , TRP B:34 , LYS B:76 , LYS B:80 , LYS B:103binding site for residue GOL B 404
8AC8SOFTWAREPHE B:233 , HIS B:235 , ARG B:245binding site for residue CL B 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5M56)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:231 -Pro A:232
2Lys B:72 -Pro B:73
3Glu B:231 -Pro B:232

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M56)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M56)

(-) Exons   (0, 0)

(no "Exon" information available for 5M56)

(-) 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:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhh....ee...eeeeeeee....eeeeeeee.....eeeeeee...hhhhhhhhhhhhhhhh.......eeeeee......eeeeee.....hhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee......ee............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh.......hhhhhh...hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m56 A   2 PGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDGYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQ 332
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331 


Chain B from PDB  Type:PROTEIN  Length:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhh....ee...eeeeee........eeeeee....eeeeeee....hhhhhhhhhhhhhhhh.......eeeeee......eeeeee.....hhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee......ee............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh.......hhhhhh...hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m56 B   6 AGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDGYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQS 333
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325
   Legend:   → Mismatch (orange background)
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  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 5M56)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M56)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M56)

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)

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  5m56
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        CSK22_HUMAN | P19784: 3e3b 3ofm 3u87 5m4u

(-) Related Entries Specified in the PDB File

5m4u THE SAME COMPLEX CRYSTALLIZED WITH A DIFFERENT CRYSTAL PACKING (ORTHORHOMBIC SPACE GROUP).