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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN VACCINIA-RELATED KINASE BOUND TO BI-D1870
 
Authors :  R. M. Counago, C. Bountra, P. Arruda, A. M. Edwards, O. Gileadi, Structu Genomics Consortium (Sgc)
Date :  20 Feb 17  (Deposition) - 22 Mar 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Transferase, Protein Kinase Domain, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. M. Counago, C. Bountra, P. Arruda, A. M. Edwards, O. Gileadi, Structural Genomics Consortium (Sgc)
Crystal Structure Of The Human Vaccinia-Related Kinase Boun To Bi-D1870
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE VRK1
    Chains: A, B, C, D
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: DE3
    Expression System Taxid: 562
    Expression System Variant: R3
    Fragment: UNP RESIDUES 3-364
    Gene: VRK1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: VACCINIA-RELATED KINASE 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
17DZ4Ligand/Ion(7S)-2-[(3,5-DIFLUORO-4-HYDROXYPHENYL)AMINO]-5,7-DIMETHYL-8-(3-METHYLBUTYL)-7,8-DIHYDROPTERIDIN-6(5H)-ONE
2CL1Ligand/IonCHLORIDE ION
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PO410Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
17DZ1Ligand/Ion(7S)-2-[(3,5-DIFLUORO-4-HYDROXYPHENYL)AMINO]-5,7-DIMETHYL-8-(3-METHYLBUTYL)-7,8-DIHYDROPTERIDIN-6(5H)-ONE
2CL-1Ligand/IonCHLORIDE ION
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
4PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
17DZ1Ligand/Ion(7S)-2-[(3,5-DIFLUORO-4-HYDROXYPHENYL)AMINO]-5,7-DIMETHYL-8-(3-METHYLBUTYL)-7,8-DIHYDROPTERIDIN-6(5H)-ONE
2CL-1Ligand/IonCHLORIDE ION
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 3 (3, 6)
No.NameCountTypeFull Name
17DZ1Ligand/Ion(7S)-2-[(3,5-DIFLUORO-4-HYDROXYPHENYL)AMINO]-5,7-DIMETHYL-8-(3-METHYLBUTYL)-7,8-DIHYDROPTERIDIN-6(5H)-ONE
2CL-1Ligand/IonCHLORIDE ION
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PO44Ligand/IonPHOSPHATE ION
Biological Unit 4 (2, 4)
No.NameCountTypeFull Name
17DZ1Ligand/Ion(7S)-2-[(3,5-DIFLUORO-4-HYDROXYPHENYL)AMINO]-5,7-DIMETHYL-8-(3-METHYLBUTYL)-7,8-DIHYDROPTERIDIN-6(5H)-ONE
2CL-1Ligand/IonCHLORIDE ION
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
4PO43Ligand/IonPHOSPHATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:43 , VAL A:69 , GLU A:83 , TYR A:87 , PRO A:111 , MET A:131 , ASP A:132 , PHE A:134 , LEU A:184 , VAL A:196 , HOH A:501binding site for residue 7DZ A 401
02AC2SOFTWAREARG A:148 , HIS A:258 , HOH A:513binding site for residue PO4 A 402
03AC3SOFTWAREASP A:120 , ASN A:122 , ARG D:89 , ARG D:203binding site for residue PO4 A 403
04AC4SOFTWAREARG B:151 , GLY B:297 , ALA B:330 , HOH B:543 , PRO D:291 , ALA D:292binding site for residue PO4 B 401
05AC5SOFTWARELYS B:71 , MET B:131 , ASP B:132 , PHE B:134 , SER B:181 , HOH B:501binding site for residue 7DZ B 402
06AC6SOFTWAREGLN C:95 , HIS C:171 , HOH C:508binding site for residue PO4 C 401
07AC7SOFTWAREILE C:43 , ILE C:51 , VAL C:69 , LYS C:71 , GLU C:83 , PRO C:111 , MET C:131 , ASP C:132 , ARG C:133 , PHE C:134 , SER C:181 , LEU C:184 , VAL C:196 , ASP C:197 , HOH C:501binding site for residue 7DZ C 402
08AC8SOFTWAREARG B:89 , ARG B:203 , ARG C:241 , ARG C:279 , HOH C:523 , HOH C:611binding site for residue PO4 C 403
09AC9SOFTWARELYS C:85 , ARG C:89 , ARG C:203binding site for residue PO4 C 404
10AD1SOFTWARETYR C:202 , LYS C:211 , ARG C:219binding site for residue PO4 C 405
11AD2SOFTWAREILE C:230 , ASP C:231 , ARG C:241 , GLU C:245 , ARG C:279 , VAL C:306 , LYS C:307 , HOH C:528 , HOH C:559binding site for residue PEG C 406
12AD3SOFTWAREARG C:148 , HIS C:258binding site for residue CL C 407
13AD4SOFTWAREASN B:294 , ARG D:148 , HIS D:258 , HOH D:553binding site for residue PO4 D 401
14AD5SOFTWAREGLN D:95 , LYS D:98 , HIS D:171 , HOH D:505binding site for residue PO4 D 402
15AD6SOFTWAREILE D:43 , VAL D:69 , LYS D:71 , PRO D:111 , MET D:131 , ASP D:132 , ARG D:133 , PHE D:134 , LEU D:184 , VAL D:196 , ASP D:197 , HOH D:501binding site for residue 7DZ D 403
16AD7SOFTWAREARG D:89binding site for residue PO4 D 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UVF)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee.....eeeeeee...eeeeee...........eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeeee.eeeehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee......eee.........hhhhh...................hhhhhh....hhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uvf A  20 AEQFAVGEIITDMAAAAWKVGLPIGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDL 341
                                    29        39   ||   54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       
                                                  43|                                                                                                                                                                                                                                                                                                    
                                                   49                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.....eeeeeeee.eeeeeee...........eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeeeee..eeeeeeeee.eeeehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee......eee......ee.hhhhh...................hhhhhh....hhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uvf B  21 EQFAVGEIITDMAAAAWKVGLPIGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDL 341
                                    30        40  ||    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       335      
                                                 43|                                                                                                                                                                                                                                                                                                    
                                                  49                                                                                                                                                                                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:301
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.....eeeeeeeee..eeeeee....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee..eeeeeee....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.......eee......ee.hhhhh......hhhhh........hhhhhh....hhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uvf C  23 FAVGEIITDMAAAAWKVGLPIGQCIYLADMNDAPCVVKVEPSGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDL 341
                                    32        42  ||    56||      73 ||     85        95       105       115   ||  130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340 
                                                 45|     57|        75|                                      119|                                                                                                                                                                                                                        
                                                  50      65         78                                       125                                                                                                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.....eeeeeee...eeee.....eeeee....hhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee....eeeee.eeeehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee..eeeeeee......ee.hhhhh......hhhhh........hhhhhh....hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uvf D  25 VGEIITDMAAAAWKVGLPIGCIYLADMDAPCVVKVEPSGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDL 341
                                    34        44|     ||67       |79        89        99       109       119||     135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335      
                                              44|    56|        75|                                       120|                                                                                                                                                                                                                      
                                               50     65         78                                        127
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  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 5UVF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

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        VRK1_HUMAN | Q99986: 2kty 2kul 2lav 2rsv 3op5 5ukf

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