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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CDK8/CYCC IN COMPLEX WITH COMPOUND 5 (1-[3-TERT-BUTYL-1-(4-METHYLPHENYL)-1H-PYRAZOL-5-YL]-3-[3-(MORPHOLIN-4-YL) PROPYL]UREA)
 
Authors :  E. V. Schneider, J. Boettcher, R. Huber, K. Maskos
Date :  15 May 12  (Deposition) - 01 May 13  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Kinase Complex, Proteros, Transferase-Transcription-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. V. Schneider, J. Bottcher, R. Huber, K. Maskos, L. Neumann
Structure-Kinetic Relationship Study Of Cdk8/Cycc Specific Compounds.
Proc. Natl. Acad. Sci. Usa V. 110 8081 2013
PubMed-ID: 23630251  |  Reference-DOI: 10.1073/PNAS.1305378110

(-) Compounds

Molecule 1 - CYCLIN-DEPENDENT KINASE 8
    Chains: A
    EC Number: 2.7.11.22, 2.7.11.23
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 1-403
    Gene: CDK8
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CELL DIVISION PROTEIN KINASE 8, MEDIATOR COMPLEX SUBUNIT CDK8, MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT CDK8, PROTEIN KINASE K35
 
Molecule 2 - CYCLIN-C
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: CCNC
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SRB11 HOMOLOG, HSRB11

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 19)

Asymmetric/Biological Unit (5, 19)
No.NameCountTypeFull Name
10SR1Ligand/Ion1-[3-TERT-BUTYL-1-(4-METHYLPHENYL)-1H-PYRAZOL-5-YL]-3-[3-(MORPHOLIN-4-YL)PROPYL]UREA
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO10Ligand/Ion1,2-ETHANEDIOL
4FMT6Ligand/IonFORMIC ACID
5NA1Ligand/IonSODIUM ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:32 , ALA A:50 , SER A:62 , ARG A:65 , GLU A:66 , LEU A:73 , ILE A:79 , PHE A:97 , ASP A:98 , ALA A:100 , ILE A:171 , ALA A:172 , ASP A:173 , HOH A:668BINDING SITE FOR RESIDUE 0SR A 501
02AC2SOFTWAREHIS A:75 , ASP A:137 , HIS A:140 , HOH A:765BINDING SITE FOR RESIDUE NA A 502
03AC3SOFTWAREPRO A:164 , ARG A:166 , ARG A:168 , SER A:343BINDING SITE FOR RESIDUE DMS A 503
04AC4SOFTWAREARG A:71 , GLU A:72 , GLN B:7 , LEU B:12 , GLN B:13BINDING SITE FOR RESIDUE EDO A 504
05AC5SOFTWAREHIS A:249 , ASP A:282 , PHE A:283 , THR A:287 , TYR A:288 , HOH A:707BINDING SITE FOR RESIDUE EDO A 505
06AC6SOFTWARELEU A:70 , ARG A:71 , LEU A:81 , EDO A:507 , HOH A:667BINDING SITE FOR RESIDUE EDO A 506
07AC7SOFTWAREARG A:71 , LYS A:83 , VAL A:84 , EDO A:506 , ASP B:147BINDING SITE FOR RESIDUE EDO A 507
08AC8SOFTWAREPRO A:124 , GLY A:126 , MET A:127BINDING SITE FOR RESIDUE EDO A 508
09AC9SOFTWAREVAL A:16 , GLU A:17 , TYR A:22 , GLN A:53 , SER A:87 , ASP A:90 , LYS A:92 , TRP A:94BINDING SITE FOR RESIDUE EDO A 509
10BC1SOFTWAREARG A:65 , ARG A:150BINDING SITE FOR RESIDUE FMT A 511
11BC2SOFTWAREALA B:0 , ALA B:2 , ILE B:151 , VAL B:152 , TYR B:153 , HOH B:442BINDING SITE FOR RESIDUE EDO B 301
12BC3SOFTWAREASN B:46 , ARG B:185 , TRP B:241 , PHE B:244 , GLU B:246BINDING SITE FOR RESIDUE EDO B 302
13BC4SOFTWAREGLN B:161 , TYR B:162BINDING SITE FOR RESIDUE EDO B 303
14BC5SOFTWAREASN B:243BINDING SITE FOR RESIDUE EDO B 304
15BC6SOFTWAREGLN B:41 , THR B:45 , THR B:66 , LYS B:70 , TYR B:184 , FMT B:307BINDING SITE FOR RESIDUE FMT B 305
16BC7SOFTWAREHIS B:54 , LEU B:55 , ARG B:107 , HOH B:444BINDING SITE FOR RESIDUE FMT B 306
17BC8SOFTWARETYR B:37 , GLN B:41 , FMT B:305 , HOH B:478BINDING SITE FOR RESIDUE FMT B 307
18BC9SOFTWARELYS B:126 , GLU B:127 , PRO B:129 , HOH B:506 , HOH B:513BINDING SITE FOR RESIDUE FMT B 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F6U)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:338 -Pro A:339

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F6U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F6U)

(-) Exons   (0, 0)

(no "Exon" information available for 4F6U)

(-) 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:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.hhhhhee....eeee...eeeeeeee........eeeeee.....hhhhhhhhhhhhhh.........eeeee....eeeeeee...eehhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.........eee............hhhhhh.....hhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhh..hhhhh.hhhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f6u A  -1 DKMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQENPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFL 359
                                     8        18        28        38        48        58        68        78        88        98       108      |123       133       143       153       163       173  ||   200       210       220       230       245       255       265       275       285       295       305       315       325       335       345       355    
                                                                                                                                              115|                                                    176|                                          239|                                                                                                                  
                                                                                                                                               121                                                     194                                           245                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f6u B  -2 DKAMAGNFWQSSHYLQWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFSYAFPKEFPYRMNHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQWFAELSVDMEKILEIIRVILKLYEQWKNFDERKEMATILSKMPKPKPPP 264
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257
   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 4F6U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F6U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F6U)

(-) Gene Ontology  (27, 37)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:338 - Pro A:339   [ RasMol ]  
 

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  CDK8_HUMAN | P49336
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 Related Entries

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

UniProtKB/Swiss-Prot
        CCNC_HUMAN | P24863: 3rgf 4crl 4f6s 4f6w 4f70 4f7j 4f7l 4f7n 4f7s 4g6l 5bnj 5cei 5fgk 5hbe 5hbh 5hbj 5hnb 5hvy 5i5z 5icp 5idn 5idp
        CDK8_HUMAN | P49336: 3rgf 4crl 4f6s 4f6w 4f70 4f7j 4f7l 4f7n 4f7s 4g6l 5bnj 5cei 5fgk 5hbe 5hbh 5hbj 5hnb 5hvy 5i5z 5icp 5idn 5idp

(-) Related Entries Specified in the PDB File

4f6s 4f6w 4f70 4f7j 4f7l 4f7n