2WWI - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH AZTMP AND ADP

Authors :   J. L. Whittingham, J. Carrero-Lerida, J. A. Brannigan, L. M. Ruiz-Perez, A. P. G. Silva, M. J. Fogg, A. J. Wilkinson, I. H. Gilbert, K. S. Wilson, D. Gonzalez-Pacanowska

Date :   23 Oct 09 (Deposition) - 21 Apr 10 (Release) - 21 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.99

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

Keywords :   Transferase, Kinase, Malaria (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. L. Whittingham, J. Carrero-Lerida, J. A. Brannigan, L. M. Ruiz-Perez, A. P. G. Silva, M. J. Fogg, A. J. Wilkinson, I. H. Gilbert, K. S. Wilson, D. Gonzalez-Pacanowska
Structural Basis For The Efficient Phosphorylation Of Aztmp And Dgmp By Plasmodium Falciparum Type I Thymidylate Kinase.
Biochem. J. V. 428 499 2010
PubMed-ID: 20353400 | Reference-DOI: 10.1042/BJ20091880

Molecule 1 - THYMIDILATE KINASE, PUTATIVE
	Chains	:	A, B, C
	EC Number	:	2.7.4.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	36329
	Strain	:	3D7

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	ADP	3	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	ATM	3	Ligand/Ion	3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	ATM	2	Ligand/Ion	3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	ATM	2	Ligand/Ion	3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:17 , PHE A:44 , PRO A:45 , ARG A:47 , PHE A:74 , ARG A:78 , ARG A:99 , GLY A:104 , TYR A:107 , GLU A:151 , HOH A:2003	BINDING SITE FOR RESIDUE ATM A 211
2	AC2	SOFTWARE	ARG A:18 , SER A:19 , GLY A:20 , LYS A:21 , SER A:22 , THR A:23 , ARG A:145 , ARG A:182 , ILE A:184 , HOH A:2014 , ALA B:170 , HIS B:171	BINDING SITE FOR RESIDUE ADP A 212
3	AC3	SOFTWARE	ASP B:17 , PRO B:45 , ARG B:47 , PHE B:74 , ARG B:78 , ARG B:99 , GLY B:104 , TYR B:107	BINDING SITE FOR RESIDUE ATM B 211
4	AC4	SOFTWARE	ARG B:18 , SER B:19 , GLY B:20 , LYS B:21 , SER B:22 , THR B:23 , ARG B:182 , ILE B:184 , HOH B:2001	BINDING SITE FOR RESIDUE ADP B 212
5	AC5	SOFTWARE	ASP C:17 , PHE C:44 , PRO C:45 , ARG C:47 , LEU C:59 , PHE C:74 , ARG C:78 , ARG C:99 , GLY C:104 , TYR C:107 , TYR C:153	BINDING SITE FOR RESIDUE ATM C 211
6	AC6	SOFTWARE	ARG C:18 , SER C:19 , GLY C:20 , LYS C:21 , SER C:22 , THR C:23 , ARG C:145 , ARG C:182 , ILE C:184 , ILE C:187	BINDING SITE FOR RESIDUE ADP C 212

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

Asymmetric Unit

No.	Residues
1	Phe A:44	-	Pro A:45
2	Leu A:208	-	Trp A:209
3	Phe B:44	-	Pro B:45
4	Leu B:208	-	Trp B:209
5	Phe C:44	-	Pro C:45
6	Leu C:208	-	Trp C:209

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

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

(no "Exon" information available for 2WWI)

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:208
 aligned with Q8I4S1_PLAF7 | Q8I4S1 from UniProtKB/TrEMBL  Length:210

    Alignment length:208
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202        
         Q8I4S1_PLAF7     3 DDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNRSDYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
               SCOP domains d2wwia_ A: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2wwiA00 A:3-210 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhh..hhhhhhh.........eeeeee....hhhhh.........hhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wwi A   3 DDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNRSDYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202

Chain B from PDB  Type:PROTEIN  Length:197
 aligned with Q8I4S1_PLAF7 | Q8I4S1 from UniProtKB/TrEMBL  Length:210

    Alignment length:207
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       
         Q8I4S1_PLAF7     3 DDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNRSDYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLW 209
               SCOP domains d2wwib_ B: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains 2wwiB00 B:3-209 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh...hhhhhhhhhh......eeeeee......-------......hhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh.---.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wwi B   3 DDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYA-------EEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVT---VEPEEFNFLW 209
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192   |   202       
                                                                                                                                                                     142     150                                           196 200

Chain C from PDB  Type:PROTEIN  Length:205
 aligned with Q8I4S1_PLAF7 | Q8I4S1 from UniProtKB/TrEMBL  Length:210

    Alignment length:208
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202        
         Q8I4S1_PLAF7     3 DDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNRSDYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
               SCOP domains d2wwic_ C: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2wwiC00 C:3-210 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                             CATH domains
           Pfam domains (1) ----------Thymidylate_kin-2wwiC01 C:13-191                                                                                                                                                   -----  ------------ Pfam domains (1)
           Pfam domains (2) ----------Thymidylate_kin-2wwiC02 C:13-191                                                                                                                                                   -----  ------------ Pfam domains (2)
           Pfam domains (3) ----------Thymidylate_kin-2wwiC03 C:13-191                                                                                                                                                   -----  ------------ Pfam domains (3)
         Sec.struct. author .......eeeeee....hhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhh..hhhhhhh.........eeeeee....hhhhh-........hhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhh--............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wwi C   3 DDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNR-DYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVT--KVEPEEFNFLWS 210
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142  | |  152       162       172       182       192   |  |202        
                                                                                                                                                                        145 |                                              196  |           
                                                                                                                                                                          147                                                 199

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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: automated matches (303)

Protein domain: automated matches (303)

Plasmodium falciparum [TaxId: 36329] (8)

1a	d2wwia_	A:
1b	d2wwib_	B:
1c	d2wwic_	C:

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)

Plasmodium falciparum. Organism_taxid: 36329. Strain: 3d7. (4)

1a	2wwiA00	A:3-210
1b	2wwiB00	B:3-209
1c	2wwiC00	C:3-210

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Thymidylate_kin (26)

Plasmodium falciparum (isolate 3D7) (4)

1a	Thymidylate_kin-2wwiC01	C:13-191
1b	Thymidylate_kin-2wwiC02	C:13-191
1c	Thymidylate_kin-2wwiC03	C:13-191

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q8I4S1_PLAF7 | Q8I4S1)

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: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:0009041	uridylate kinase activity	Catalysis of the reaction: ATP + (d)UMP = ADP + (d)UDP.
biological process
	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: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.
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: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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	Cis Peptide Bonds
		Leu A:208 - Trp A:209	[ RasMol ]
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		Phe C:44 - Pro C:45	[ RasMol ]

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	2wwi
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	Q8I4S1_PLAF7 \| Q8I4S1	:	2wwf 2wwg 2wwh 2yof 2yog 2yoh

2wwf	PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH TMP AND ADP
2wwg	PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH DGMP AND ADP
2wwh	PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH AP5DT

Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

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