2YOF - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH A (THIO)UREA-BETA-DEOXYTHYMIDINE INHIBITOR

Authors :   C. Huaqing, J. Carrero-Lerida, A. P. G. Silva, J. L. Whittingham, J. A. B L. M. Ruiz-Perez, K. D. Read, K. S. Wilson, D. Gonzalez-Pacanowska, I. H. Gilbert

Date :   24 Oct 12 (Deposition) - 24 Jul 13 (Release) - 24 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.82

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

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

Reference :   H. Cui, J. Carrero-Lerida, A. P. G. Silva, J. L. Whittingham, J. A. Brannigan, L. M. Ruiz-Perez, K. D. Read, K. S. Wilson, D. Gonzalez-Pacanowska, I. H. Gilbert
Synthesis And Evaluation Of Alpha-Thymidine Analogues As Novel Antimalarials.
J. Med. Chem. V. 55 10948 2012
PubMed-ID: 23240776 | Reference-DOI: 10.1021/JM301328H

Molecule 1 - THYMIDYLATE KINASE
	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
	Expression System Vector	:	PET28
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	36329
	Strain	:	3D7

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	74W	3	Ligand/Ion	1-[4-CHLORANYL-3-(TRIFLUOROMETHYL)PHENYL]-3-[[(2R,3S)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHYL]THIOUREA
2	ACT	5	Ligand/Ion	ACETATE ION
3	TAM	2	Ligand/Ion	TRIS(HYDROXYETHYL)AMINOMETHANE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	74W	1	Ligand/Ion	1-[4-CHLORANYL-3-(TRIFLUOROMETHYL)PHENYL]-3-[[(2R,3S)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHYL]THIOUREA
2	ACT	1	Ligand/Ion	ACETATE ION
3	TAM	1	Ligand/Ion	TRIS(HYDROXYETHYL)AMINOMETHANE

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	74W	1	Ligand/Ion	1-[4-CHLORANYL-3-(TRIFLUOROMETHYL)PHENYL]-3-[[(2R,3S)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHYL]THIOUREA
2	ACT	1	Ligand/Ion	ACETATE ION
3	TAM	1	Ligand/Ion	TRIS(HYDROXYETHYL)AMINOMETHANE

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	74W	1	Ligand/Ion	1-[4-CHLORANYL-3-(TRIFLUOROMETHYL)PHENYL]-3-[[(2R,3S)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHYL]THIOUREA
2	ACT	3	Ligand/Ion	ACETATE ION
3	TAM	-1	Ligand/Ion	TRIS(HYDROXYETHYL)AMINOMETHANE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:17 , ARG A:18 , PHE A:44 , ARG A:47 , LEU A:59 , PHE A:74 , ARG A:78 , ARG A:99 , GLY A:104 , TYR A:107 , GLU A:150 , GLU A:151 , TYR A:153 , GLU A:154 , HOH A:2072 , HOH A:2117 , HOH A:2148 , HOH A:2180	BINDING SITE FOR RESIDUE 74W A 211
02	AC2	SOFTWARE	ASP B:17 , ARG B:47 , LEU B:59 , PHE B:74 , ARG B:78 , ARG B:99 , GLY B:104 , TYR B:107 , GLU B:150 , GLU B:151 , TYR B:153 , GLU B:154 , HOH B:2117 , HOH B:2146 , HOH B:2190	BINDING SITE FOR RESIDUE 74W B 211
03	AC3	SOFTWARE	ASP C:17 , SER C:22 , PRO C:45 , ARG C:47 , LEU C:59 , PHE C:74 , ARG C:78 , ARG C:99 , SER C:103 , GLY C:104 , TYR C:107 , TYR C:148 , TYR C:153 , ACT C:1212 , HOH C:2012 , HOH C:2018 , HOH C:2048 , HOH C:2084 , HOH C:2105 , HOH C:2135 , HOH C:2137	BINDING SITE FOR RESIDUE 74W C 211
04	AC4	SOFTWARE	LEU A:42 , TYR A:43 , ASN A:46 , HIS A:81	BINDING SITE FOR RESIDUE ACT A1211
05	AC5	SOFTWARE	LEU B:42 , TYR B:43 , ASN B:46 , HIS B:81	BINDING SITE FOR RESIDUE ACT B1211
06	AC6	SOFTWARE	LEU C:42 , TYR C:43 , ASN C:46 , HIS C:81	BINDING SITE FOR RESIDUE ACT C1211
07	AC7	SOFTWARE	ASP C:17 , ARG C:18 , SER C:19 , GLY C:20 , LYS C:21 , SER C:22 , TYR C:148 , 74W C:211 , ACT C:1213 , HOH C:2017	BINDING SITE FOR RESIDUE ACT C1212
08	AC8	SOFTWARE	GLY C:20 , SER C:22 , THR C:23 , ARG C:145 , TYR C:148 , ACT C:1212	BINDING SITE FOR RESIDUE ACT C1213
09	AC9	SOFTWARE	LEU A:16 , ARG A:18 , SER A:19 , GLY A:20 , LYS A:21 , SER A:22 , THR A:23	BINDING SITE FOR RESIDUE TAM A1212
10	BC1	SOFTWARE	LEU B:16 , ARG B:18 , SER B:19 , GLY B:20 , LYS B:21 , SER B:22 , HOH B:2025	BINDING SITE FOR RESIDUE TAM B1212

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

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 2YOF)

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

(no "Exon" information available for 2YOF)

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:200
 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 d2yofa_ A: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhh.hhhhhhhhhh......eeeeee.....--------.....hhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yof A   3 DDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNY--------EEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
                                    12        22        32        42        52        62        72        82        92       102       112       122       132        |-       152       162       172       182       192       202        
                                                                                                                                                                    141      150

Chain B from PDB  Type:PROTEIN  Length:204
 aligned with Q8I4S1_PLAF7 | Q8I4S1 from UniProtKB/TrEMBL  Length:210

    Alignment length:210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
         Q8I4S1_PLAF7     1 MTDDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNRSDYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
               SCOP domains d2yofb_ B: automated matches                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeee....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhh..hhhhhhhhhh......eeeeee.......------.....hhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yof B   1 MTDDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQ------EEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  |    150       160       170       180       190       200       210
                                                                                                                                                                        143    150

Chain C 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 d2yofc_ C: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhh..hhhhhhhhhh......eeeeee..................hhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yof C   3 DDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNRSDYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202

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	d2yofa_	A:
1b	d2yofb_	B:
1c	d2yofc_	C:

(no "CATH Domain" information available for 2YOF)

(no "Pfam Domain" information available for 2YOF)

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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	Ligands, Modified Residues, Ions
		74W	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TAM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		BC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Leu A:208 - Trp A:209	[ RasMol ]
		Leu B:208 - Trp B:209	[ RasMol ]
		Leu C:208 - Trp C:209	[ RasMol ]
		Phe A:44 - Pro A:45	[ RasMol ]
		Phe B:44 - Pro B:45	[ RasMol ]
		Phe C:44 - Pro C:45	[ RasMol ]

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		Biological Unit 3	[ Jena3D ]

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	2yof
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	2.7.4.9
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UniProtKB/TrEMBL
	Q8I4S1_PLAF7 \| Q8I4S1	:	2wwf 2wwg 2wwh 2wwi 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
2wwi	PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH AZTMP AND ADP
2yog	PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH A (THIO)UREA-ALPHA-DEOXYTHYMIDINE INHIBITOR
2yoh	PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH A UREA-ALPHA-DEOXYTHYMIDINE INHIBITOR

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 3)

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Gene Ontology (13, 13)

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