2NO0 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   C4S DCK VARIANT OF DCK IN COMPLEX WITH GEMCITABINE+ADP

Authors :   E. Sabini, S. Hazra, M. Konrad, S. K. Burley, A. Lavie

Date :   24 Oct 06 (Deposition) - 03 Jul 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A (2x),B (2x)
Biol. Unit 3: A,B  (2x)

Keywords :   Dck, Gemcitabine, Human Deoxycytidine Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Sabini, S. Hazra, M. Konrad, A. Lavie
Nonenantioselectivity Property Of Human Deoxycytidine Kinase Explained By Structures Of The Enzyme In Complex With L- And D-Nucleosides.
J. Med. Chem. V. 50 3004 2007
PubMed-ID: 17530837 | Reference-DOI: 10.1021/JM0700215
(for further references see the PDB file header)

Molecule 1 - DEOXYCYTIDINE KINASE
	Chains	:	A, B
	EC Number	:	2.7.1.74
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET14B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DCK
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DCK

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A (2x)	B (2x)
Biological Unit 3 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	GEO	2	Ligand/Ion	GEMCITABINE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	GEO	2	Ligand/Ion	GEMCITABINE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	GEO	2	Ligand/Ion	GEMCITABINE

Biological Unit 3 (2, 8)

No.	Name	Count	Type	Full Name
1	ADP	4	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	GEO	4	Ligand/Ion	GEMCITABINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:31 , ALA A:32 , GLY A:33 , LYS A:34 , SER A:35 , THR A:36 , ARG A:188 , ARG A:192 , GLU A:240 , ASP A:241 , PHE A:242 , HOH A:339 , HOH A:370 , HOH A:396 , HOH A:398 , HOH A:421 , ASP B:241 , PHE B:242	BINDING SITE FOR RESIDUE ADP A 301
2	AC2	SOFTWARE	ILE A:30 , GLU A:53 , TRP A:58 , MET A:85 , TYR A:86 , PHE A:96 , GLN A:97 , ARG A:128 , ASP A:133 , PHE A:137 , GLU A:197 , HOH A:373 , HOH A:398 , HOH A:419	BINDING SITE FOR RESIDUE GEO A 302
3	AC3	SOFTWARE	ASP A:241 , LYS A:243 , HOH A:344 , HOH A:421 , ALA B:31 , ALA B:32 , GLY B:33 , LYS B:34 , SER B:35 , THR B:36 , ARG B:188 , ARG B:192 , GLU B:240 , ASP B:241 , PHE B:242 , TYR B:246 , HOH B:395 , HOH B:398 , HOH B:404 , HOH B:408	BINDING SITE FOR RESIDUE ADP B 301
4	AC4	SOFTWARE	ILE B:30 , GLU B:53 , TRP B:58 , LEU B:82 , MET B:85 , TYR B:86 , PHE B:96 , GLN B:97 , ARG B:128 , ASP B:133 , PHE B:137 , GLU B:197 , HOH B:404 , HOH B:406	BINDING SITE FOR RESIDUE GEO B 302

(no "SS Bond" information available for 2NO0)

(no "Cis Peptide Bond" information available for 2NO0)

(no "SAP(SNP)/Variant" information available for 2NO0)

(no "PROSITE Motif" information available for 2NO0)

Asymmetric Unit (7, 14)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3a	ENST00000286648	3a	ENSE00002041408	chr4:71859156-71859643	488	DCK_HUMAN	1-31	31	2	A:19-31 B:20-31	13 12
1.4	ENST00000286648	4	ENSE00001024728	chr4:71863784-71863899	116	DCK_HUMAN	31-69	39	2	A:31-69 B:31-64	39 34
1.5	ENST00000286648	5	ENSE00001024734	chr4:71888084-71888277	194	DCK_HUMAN	70-134	65	2	A:70-134 B:77-134 (gaps)	65 58
1.6	ENST00000286648	6	ENSE00001024731	chr4:71889276-71889423	148	DCK_HUMAN	134-183	50	2	A:134-183 B:134-183	50 50
1.7a	ENST00000286648	7a	ENSE00001024724	chr4:71891533-71891648	116	DCK_HUMAN	184-222	39	2	A:184-222 B:184-222	39 39
1.8a	ENST00000286648	8a	ENSE00001076634	chr4:71892382-71892472	91	DCK_HUMAN	222-252	31	2	A:222-252 B:222-252 (gaps)	31 31
1.10	ENST00000286648	10	ENSE00001235483	chr4:71895069-71896631	1563	DCK_HUMAN	253-260	8	2	A:253-260 B:253-260	8 8

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:242
 aligned with DCK_HUMAN | P27707 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:242
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258  
            DCK_HUMAN    19 TRIKKISIEGNIAAGKSTFVNILKQLCEDWEVVPEPVARWCNVQSTQDEFEELTMSQKNGGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFASNLYESECMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKYESLVEKVKEFLSTL 260
               SCOP domains d2no0a_ A: Deoxycytidine kinase                                                                                                                                                                                                                    SCOP domains
               CATH domains 2no0A00 A:19-260 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhhhhhhh..eeee..hhhhhhh.......hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhh..eeeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a    --------------------------------------Exon 1.5  PDB: A:70-134 UniProt: 70-134                          -------------------------------------------------Exon 1.7a  PDB: A:184-222              ------------------------------1.10     Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.4  PDB: A:31-69 UniProt: 31-69  ----------------------------------------------------------------Exon 1.6  PDB: A:134-183 UniProt: 134-183         --------------------------------------Exon 1.8a  PDB: A:222-252      -------- Transcript 1 (2)
                 2no0 A  19 TRIKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSNVQSTQDEFEELTMSQKNGGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFASNLYESESMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKYESLVEKVKEFLSTL 260
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258

Chain B from PDB  Type:PROTEIN  Length:225
 aligned with DCK_HUMAN | P27707 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:241
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259 
            DCK_HUMAN    20 RIKKISIEGNIAAGKSTFVNILKQLCEDWEVVPEPVARWCNVQSTQDEFEELTMSQKNGGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFASNLYESECMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKDKYESLVEKVKEFLSTL 260
               SCOP domains d2no0b_ B: Deoxycytidine kinase                                                                                                                                                                                                                   SCOP domains
               CATH domains 2no0B00 B:20-260 P-loop containing nucleotide             triphosphate hydrolases                                                                                                                                                                 CATH domains
           Pfam domains (1) ---------------------------------------------            -------------------dNK-2no0B01 B:96-253                                                                                                                                          ------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------            -------------------dNK-2no0B02 B:96-253                                                                                                                                          ------- Pfam domains (2)
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhh..eeee..hhhhhhh....------------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-.....eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhh.eeeee.....---hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a   --------------------------------------Exon 1.5  PDB: B:77-134 (gaps) UniProt: 70-134 [INCOMPLETE]      -------------------------------------------------Exon 1.7a  PDB: B:184-222              ------------------------------1.10     Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.4  PDB: B:31-64 UniProt: 31-69  ----------------------------------------------------------------Exon 1.6  PDB: B:134-183 UniProt: 134-183         --------------------------------------Exon 1.8a  PDB: B:222-252 (gaps-------- Transcript 1 (2)
                 2no0 B  20 RIKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSNVQST------------NGGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKL-DAEKPVLFFERSVYSDRYIFASNLYESESMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPILTLDVNEDF---YESLVEKVKEFLSTL 260
                                    29        39        49        59    |    -       |79        89        99       109      |119       129       139       149       159       169       179       189       199       209       219       229       239  |   |249       259 
                                                                       64           77                                    116 |                                                                                                                         242 246              
                                                                                                                            118

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Nucleotide and nucleoside kinases (231)

Protein domain: Deoxycytidine kinase (35)

Human (Homo sapiens) [TaxId: 9606] (35)

1a	d2no0a_	A:
1b	d2no0b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Human (Homo sapiens) (413)

1a	2no0B00	B:20-260
1b	2no0A00	A:19-260

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: dNK (33)

Homo sapiens (Human) (20)

1a	dNK-2no0B01	B:96-253
1b	dNK-2no0B02	B:96-253

Asymmetric Unit(hide GO term definitions)

Chain A,B (DCK_HUMAN | P27707)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004137	deoxycytidine kinase activity	Catalysis of the reaction: NTP + deoxycytidine = NDP + CMP.
	GO:0008144	drug binding	Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0019206	nucleoside kinase activity	Catalysis of the reaction: ATP + nucleoside = ADP + nucleoside monophosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0009157	deoxyribonucleoside monophosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of a deoxyribonucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with phosphate on the sugar.
	GO:0006139	nucleobase-containing compound metabolic process	Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
	GO:0009165	nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0043101	purine-containing compound salvage	Any process that generates a purine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a purine base, from derivatives of them without de novo synthesis.
	GO:0043097	pyrimidine nucleoside salvage	Any process that generates a pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose, from derivatives of it, without de novo synthesis.
	GO:0006220	pyrimidine nucleotide metabolic process	The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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1p5z	WILD TYPE HUMAN DEOXYCYTIDINE KINASE IN COMPLEX WITH CYTARABINE AND ADP-MG
1p60	WILD TYPE HUMAN DEOXYCYTIDINE KINASE IN COMPLEX WITH DEOXYCYTIDINE AND ADP
1p61	WILD TYPE HUMAN DEOXYCYTIDINE KINASE IN COMPLEX WITH DEOXYCYTIDINE AND ADP
1p62	WILD TYPE HUMAN DEOXYCYTIDINE KINASE IN COMPLEX WITH GEMCITABINE AND ADP-MG
2a2z	INSERT-DELETION MUTANT OF HUMAN DEOXYCYTIDINE KINASE IN COMPLEX WITH DEOXYCYTIDINE AND UDP
2a30	INSERT-DELETION MUTANT OF HUMAN DEOXYCYTIDINE KINASE IN COMPLEX WITH DEOXYCYTIDINE
2no1

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