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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CDK13/CYCLIN K IN COMPLEX WITH ADP-ALUMINUM FLUORIDE
 
Authors :  D. Hoenig, A. K. Greifenberg, K. Anand, M. Geyer
Date :  24 Oct 15  (Deposition) - 30 Dec 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Kinase, Cyclin, Adp, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Greifenberg, D. Honig, K. Pilarova, R. Duster, K. Bartholomeeusen, C. A. Bosken, K. Anand, D. Blazek, M. Geyer
Structural And Functional Analysis Of The Cdk13/Cyclin K Complex.
Cell Rep V. 14 320 2016
PubMed-ID: 26748711  |  Reference-DOI: 10.1016/J.CELREP.2015.12.025

(-) Compounds

Molecule 1 - CYCLIN-DEPENDENT KINASE 13
    Chains: A, C
    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
    Fragment: UNP RESIDUES 694-1039
    Gene: CDK13, CDC2L, CDC2L5, CHED, KIAA1791
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CDC2-RELATED PROTEIN KINASE 5,CELL DIVISION CYCLE 2-LIKE PROTEIN KINASE 5,CELL DIVISION PROTEIN KINASE 13,HCDK13, CHOLINESTERASE-RELATED CELL DIVISION CONTROLLER
 
Molecule 2 - CYCLIN-K
    Chains: B, D
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Gene: CCNK, CPR4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AF32Ligand/IonALUMINUM FLUORIDE
3MG4Ligand/IonMAGNESIUM ION
4TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AF31Ligand/IonALUMINUM FLUORIDE
3MG-1Ligand/IonMAGNESIUM ION
4TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AF31Ligand/IonALUMINUM FLUORIDE
3MG-1Ligand/IonMAGNESIUM ION
4TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:711 , GLY A:714 , THR A:715 , ALA A:732 , LYS A:734 , PHE A:791 , GLU A:792 , MET A:794 , ASP A:797 , SER A:841 , ASN A:842 , LEU A:844 , ASP A:855 , HIS A:1018 , AF3 A:1102 , MG A:1103 , MG A:1104 , HOH A:1207 , HOH A:1223 , HOH A:1224 , HOH A:1226 , HOH A:1227 , HOH A:1232binding site for residue ADP A 1101
2AC2SOFTWAREASP A:837 , LYS A:839 , ASN A:842 , ASP A:855 , ADP A:1101 , MG A:1103 , MG A:1104 , HOH A:1207binding site for residue AF3 A 1102
3AC3SOFTWAREASN A:842 , ASP A:855 , ADP A:1101 , AF3 A:1102 , HOH A:1207binding site for residue MG A 1103
4AC4SOFTWAREASP A:855 , ADP A:1101 , AF3 A:1102 , HOH A:1204binding site for residue MG A 1104
5AC5SOFTWAREILE C:711 , GLU C:713 , GLY C:714 , THR C:715 , ALA C:732 , LYS C:734 , PHE C:791 , GLU C:792 , MET C:794 , ASP C:797 , SER C:841 , ASN C:842 , LEU C:844 , ASP C:855 , HIS C:1018 , AF3 C:1102 , MG C:1103 , MG C:1104 , HOH C:1202 , HOH C:1203 , HOH C:1241 , HOH C:1244 , HOH C:1247 , HOH C:1250binding site for residue ADP C 1101
6AC6SOFTWAREASP C:837 , LYS C:839 , ASN C:842 , ASP C:855 , ADP C:1101 , MG C:1103 , MG C:1104 , HOH C:1203binding site for residue AF3 C 1102
7AC7SOFTWAREASN C:842 , ASP C:855 , ADP C:1101 , AF3 C:1102 , HOH C:1203binding site for residue MG C 1103
8AC8SOFTWAREASP C:855 , ADP C:1101 , AF3 C:1102 , HOH C:1269binding site for residue MG C 1104

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EFQ)

(-) 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:322
                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhh.eeeeeeeee....eeeeeee.....eeeeeee.........hhhhhhhhhhhhhh.......eeeeee.....eeeeee...eehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee.hhhhhee..............hhhhhhhhhhh......hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh......hhhhhhh..............hhhhhh...hhhhhhhhhhhh........hhhhhhhh......hhhhh...........hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5efq A  695 IDWGKRCVDKFDIIGIIGEGTYGQVYKARDKDTGEMVALKKVRLDNEKEGFPITAIREIKILRQLTHQSIINMKEIVTDKEGAFYLVFEYMDHDLMGLLESGLVHFNENHIKSFMRQLMEGLDYCHKKNFLHRDIKCSNILLNNRGQIKLADFGLARLYSSEESRPYtNKVITLWYRPPELLLGEERYTPAIDVWSCGCILGELFTKKPIFQANQELAQLELISRICGSPCPAVWPDVIKLPYFNTMKPKKQYRRKLREEFVFIPAAALDLFDYMLALDPSKRCTAEQALQCEFLRDVEPSKMPPPDLPLWQDCHELWSKKR 1025
                                   704       714       724       734       744       754       764       774||     793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023  
                                                                                                          775|                                                                                   871-TPO                                                                                                                                                      
                                                                                                           785                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhh......hhhhhh....hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5efq B   21 KPCWYWDKKDLAHTPSQLEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQFVQDVPVDVLEDICHQILDLYSQGK  262
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260  


Chain C from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeeeeeee......eeeeee.....eeeeeee.........hhhhhhhhhhhhhh.......eeeeee.....eeeeee...eehhhhhh......hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee.hhhhhee..............hhhhhhhhhhh......hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh......hhhhhhh..............hhhhhh...hhhhhhhhhhhh........hhhhhhhh......hhhhh...........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5efq C  697 WGKRCVDKFDIIGIIGEGTYGQVYKARDKDTGEMVALKKVRLDNEKEGFPITAIREIKILRQLTHQSIINMKEIVTDKEGAFYLVFEYMDHDLMGLLESGLVHFNENHIKSFMRQLMEGLDYCHKKNFLHRDIKCSNILLNNRGQIKLADFGLARLYSSEESRPYtNKVITLWYRPPELLLGEERYTPAIDVWSCGCILGELFTKKPIFQANQELAQLELISRICGSPCPAVWPDVIKLPYFNTMKPKKQYRRKLREEFVFIPAAALDLFDYMLALDPSKRCTAEQALQCEFLRDVEPSKMPPPDLPLWQDCHELWSKKRRRQKQM 1031
                                   706       716       726       736       746       756       766       785       795       805       815       825       835       845       855       865     | 875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      
                                                                                                        775|                                                                                   871-TPO                                                                                                                                                            
                                                                                                         785                                                                                                                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                                
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhh......hhhhhh....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5efq D   21 KPCWYWDKKDLAHTPSQLEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQFVQDVPVDVLEDICHQILDLYS  259
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   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 5EFQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (46, 54)

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  5efq
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  CDK13_HUMAN | Q14004
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        CCNK_HUMAN | O75909: 2i53 4cxa 4nst 4un0 5acb

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