5UVF - JenaLib

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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

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

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
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)

Asymmetric Unit (4, 16)

No.	Name	Count	Type	Full Name
1	7DZ	4	Ligand/Ion	(7S)-2-[(3,5-DIFLUORO-4-HYDROXYPHENYL)AMINO]-5,7-DIMETHYL-8-(3-METHYLBUTYL)-7,8-DIHYDROPTERIDIN-6(5H)-ONE
2	CL	1	Ligand/Ion	CHLORIDE ION
3	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PO4	10	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	7DZ	1	Ligand/Ion	(7S)-2-[(3,5-DIFLUORO-4-HYDROXYPHENYL)AMINO]-5,7-DIMETHYL-8-(3-METHYLBUTYL)-7,8-DIHYDROPTERIDIN-6(5H)-ONE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	7DZ	1	Ligand/Ion	(7S)-2-[(3,5-DIFLUORO-4-HYDROXYPHENYL)AMINO]-5,7-DIMETHYL-8-(3-METHYLBUTYL)-7,8-DIHYDROPTERIDIN-6(5H)-ONE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (3, 6)

No.	Name	Count	Type	Full Name
1	7DZ	1	Ligand/Ion	(7S)-2-[(3,5-DIFLUORO-4-HYDROXYPHENYL)AMINO]-5,7-DIMETHYL-8-(3-METHYLBUTYL)-7,8-DIHYDROPTERIDIN-6(5H)-ONE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PO4	4	Ligand/Ion	PHOSPHATE ION

Biological Unit 4 (2, 4)

No.	Name	Count	Type	Full Name
1	7DZ	1	Ligand/Ion	(7S)-2-[(3,5-DIFLUORO-4-HYDROXYPHENYL)AMINO]-5,7-DIMETHYL-8-(3-METHYLBUTYL)-7,8-DIHYDROPTERIDIN-6(5H)-ONE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PO4	3	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ILE 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:501	binding site for residue 7DZ A 401
02	AC2	SOFTWARE	ARG A:148 , HIS A:258 , HOH A:513	binding site for residue PO4 A 402
03	AC3	SOFTWARE	ASP A:120 , ASN A:122 , ARG D:89 , ARG D:203	binding site for residue PO4 A 403
04	AC4	SOFTWARE	ARG B:151 , GLY B:297 , ALA B:330 , HOH B:543 , PRO D:291 , ALA D:292	binding site for residue PO4 B 401
05	AC5	SOFTWARE	LYS B:71 , MET B:131 , ASP B:132 , PHE B:134 , SER B:181 , HOH B:501	binding site for residue 7DZ B 402
06	AC6	SOFTWARE	GLN C:95 , HIS C:171 , HOH C:508	binding site for residue PO4 C 401
07	AC7	SOFTWARE	ILE 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:501	binding site for residue 7DZ C 402
08	AC8	SOFTWARE	ARG B:89 , ARG B:203 , ARG C:241 , ARG C:279 , HOH C:523 , HOH C:611	binding site for residue PO4 C 403
09	AC9	SOFTWARE	LYS C:85 , ARG C:89 , ARG C:203	binding site for residue PO4 C 404
10	AD1	SOFTWARE	TYR C:202 , LYS C:211 , ARG C:219	binding site for residue PO4 C 405
11	AD2	SOFTWARE	ILE 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:559	binding site for residue PEG C 406
12	AD3	SOFTWARE	ARG C:148 , HIS C:258	binding site for residue CL C 407
13	AD4	SOFTWARE	ASN B:294 , ARG D:148 , HIS D:258 , HOH D:553	binding site for residue PO4 D 401
14	AD5	SOFTWARE	GLN D:95 , LYS D:98 , HIS D:171 , HOH D:505	binding site for residue PO4 D 402
15	AD6	SOFTWARE	ILE 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:501	binding site for residue 7DZ D 403
16	AD7	SOFTWARE	ARG D:89	binding site for residue PO4 D 404

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

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

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

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

(no "Exon" information available for 5UVF)

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

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Ligands, Modified Residues, Ions (4, 16)

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