1NMY - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN THYMIDYLATE KINASE WITH FLTMP AND APPNHP

Authors :   N. Ostermann, D. Segura-Pena, C. Meier, T. Veit, M. Monnerjahn, M. Konr A. Lavie

Date :   12 Jan 03 (Deposition) - 18 Mar 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Transferase, Thymidylate Kinase, P-Loop, Fluorothymidine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Ostermann, D. Segura-Pena, C. Meier, T. Veit, M. Monnerjahn, M. Konrad, A. Lavie
Structures Of Human Thymidylate Kinase In Complex With Prodrugs: Implications For The Structure-Based Design Of Novel Compounds
Biochemistry V. 42 2568 2003
PubMed-ID: 12614151 | Reference-DOI: 10.1021/BI027302T

Molecule 1 - SIMILAR TO THYMIDYLATE KINASE (DTMP KINASE)
	Chains	:	A
	EC Number	:	2.7.4.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3	FDM	1	Ligand/Ion	3'-FLUORO-3'-DEOXYTHYMIDINE MONOPHOSPHATE
4	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3	FDM	1	Ligand/Ion	3'-FLUORO-3'-DEOXYTHYMIDINE MONOPHOSPHATE
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3	FDM	2	Ligand/Ion	3'-FLUORO-3'-DEOXYTHYMIDINE MONOPHOSPHATE
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:18 , LYS A:19 , SER A:20 , THR A:21 , ARG A:143 , LYS A:182 , ILE A:184 , MG A:401 , HOH A:504 , HOH A:506 , HOH A:507 , HOH A:508 , HOH A:537 , HOH A:566 , HOH A:573 , HOH A:583 , HOH A:592 , HOH A:607 , HOH A:624 , HOH A:651 , HOH A:674	BINDING SITE FOR RESIDUE ADP A 302
2	AC2	SOFTWARE	ASP A:15 , ARG A:16 , GLY A:18 , LYS A:19 , SER A:20 , THR A:21 , ARG A:97 , ARG A:143 , LYS A:182 , ILE A:184 , MG A:401 , HOH A:504 , HOH A:505 , HOH A:506 , HOH A:512 , HOH A:514 , HOH A:537 , HOH A:566 , HOH A:573 , HOH A:583 , HOH A:592 , HOH A:607 , HOH A:624 , HOH A:651 , HOH A:674 , HOH A:682 , HOH A:751 , HOH A:755	BINDING SITE FOR RESIDUE ANP A 303
3	AC3	SOFTWARE	PHE A:42 , PRO A:43 , ARG A:45 , PHE A:72 , ARG A:76 , ARG A:97 , GLY A:102 , PHE A:105 , TYR A:151 , HOH A:504 , HOH A:505 , HOH A:507 , HOH A:512 , HOH A:528 , HOH A:542 , HOH A:553 , HOH A:555 , HOH A:636 , HOH A:682 , HOH A:751 , HOH A:761 , HOH A:762	BINDING SITE FOR RESIDUE FDM A 301
4	AC4	SOFTWARE	SER A:20 , ADP A:302 , ANP A:303 , HOH A:504 , HOH A:505 , HOH A:506 , HOH A:507	BINDING SITE FOR RESIDUE MG A 401
5	AC5	SOFTWARE	HOH A:501 , HOH A:502 , HOH A:503	BINDING SITE FOR RESIDUE MG A 402

(no "SS Bond" information available for 1NMY)

Asymmetric Unit

No.	Residues
1	Phe A:42	-	Pro A:43

(no "SAP(SNP)/Variant" information available for 1NMY)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMIDYLATE_KINASE	PS01331	Thymidylate kinase signature.	KTHY_HUMAN	94-106	1	A:94-106

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMIDYLATE_KINASE	PS01331	Thymidylate kinase signature.	KTHY_HUMAN	94-106	1	A:94-106

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMIDYLATE_KINASE	PS01331	Thymidylate kinase signature.	KTHY_HUMAN	94-106	2	A:94-106

Asymmetric Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000305784	1a	ENSE00001856557	chr2:242626406-242626069	338	KTHY_HUMAN	1-44	44	1	A:4-44	41
1.2b	ENST00000305784	2b	ENSE00001630292	chr2:242625292-242625184	109	KTHY_HUMAN	44-80	37	1	A:44-80	37
1.7	ENST00000305784	7	ENSE00001748052	chr2:242619734-242619644	91	KTHY_HUMAN	80-110	31	1	A:80-110	31
1.8	ENST00000305784	8	ENSE00001663158	chr2:242618064-242617867	198	KTHY_HUMAN	111-176	66	1	A:111-176	66
1.9f	ENST00000305784	9f	ENSE00001645872	chr2:242615652-242615157	496	KTHY_HUMAN	177-212	36	1	A:177-212	36

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:209
 aligned with KTHY_HUMAN | P23919 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:209
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203         
           KTHY_HUMAN     4 RRGALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELLRFPERSTEIGKLLSSYLQKKSDVEDHSVHLLFSANRWEQVPLIKEKLSQGVTLVVDRYAFSGVAFTGAKENFSLDWCKQPDVGLPKPDLVLFLQLQLADAAKRGAFGHERYENGAFQERALRCFHQLMKDTTLNWKMVDASKSIEAVHEDIRVLSEDAIRTATEKPLGELWK 212
               SCOP domains d1nmya_ A: Thymidylate kinase                                                                                                                                                                                     SCOP domains
               CATH domains 1nmyA00 A:4-212 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                              CATH domains
               Pfam domains -------Thymidylate_kin-1nmyA01 A:11-191                                                                                                                                                     --------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh....hhhhhhhhhh......eeeeee.hhhhhhh..........hhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------THYMIDYLATE_K---------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:4-44 UniProt: 1-44     -----------------------------------Exon 1.7  PDB: A:80-110        Exon 1.8  PDB: A:111-176 UniProt: 111-176                         Exon 1.9f  PDB: A:177-212            Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.2b  PDB: A:44-80              ------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1nmy A   4 RRGALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELLRFPERSTEIGKLLSSYLQKKSDVEDHSVHLLFSANRWEQVPLIKEKLSQGVTLVVDRYAFSGVAFTGAKENFSLDWCKQPDVGLPKPDLVLFLQLQLADAAKRGAFGHERYENGAFQERALRCFHQLMKDTTLNWKMVDASKSIEAVHEDIRVLSEDAIATATEKPLGELWK 212
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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(

)

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: Thymidylate kinase (34)

Human (Homo sapiens) [TaxId: 9606] (20)

d1nmya_

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)

1nmyA00

A:4-212

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Thymidylate_kin (26)

Homo sapiens (Human) (5)

Thymidylate_kin-1nmyA01

A:11-191

Asymmetric Unit(hide GO term definitions)

Chain A (KTHY_HUMAN | P23919)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0050145	nucleoside phosphate kinase activity	Catalysis of the reaction: ATP + nucleoside phosphate = ADP + nucleoside diphosphate.
	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:0004798	thymidylate kinase activity	Catalysis of the reaction: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.
	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.
	GO:0009041	uridylate kinase activity	Catalysis of the reaction: ATP + (d)UMP = ADP + (d)UDP.
biological process
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0071363	cellular response to growth factor stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus.
	GO:0006233	dTDP biosynthetic process	The chemical reactions and pathways resulting in the formation of dTDP, deoxyribosylthymine diphosphate (2'-deoxyribosylthymine5'-diphosphate).
	GO:0006235	dTTP biosynthetic process	The chemical reactions and pathways resulting in the formation of dTTP, deoxyribosylthymine triphosphate.
	GO:0006227	dUDP biosynthetic process	The chemical reactions and pathways resulting in the formation of dUDP, deoxyuridine diphosphate (2'-deoxy-5'-uridylyl phosphate).
	GO:0045445	myoblast differentiation	The process in which a relatively unspecialized cell acquires specialized features of a myoblast. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into striated muscle fibers.
	GO:0015949	nucleobase-containing small molecule interconversion	The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
	GO:0046940	nucleoside monophosphate phosphorylation	The process of introducing one or more phosphate groups into a nucleoside monophosphate to produce a polyphosphorylated nucleoside.
	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:0046939	nucleotide phosphorylation	The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
	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:0046686	response to cadmium ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cadmium (Cd) ion stimulus.
	GO:0043627	response to estrogen	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics.
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:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	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.

Asymmetric Unit
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	1nmy
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Description

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Ligands, Modified Residues, Ions (4, 5)

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