2KI5 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION

Authors :   M. S. Bennett, F. Wien, J. N. Champness, T. Batuwangala, T. Rutherford, W. C. Summers, H. Sun, G. Wright, M. R. Sanderson

Date :   12 Feb 99 (Deposition) - 04 Mar 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A,B

Keywords :   Transferase (Phosphotransferase) Thymid, Transferase (Phosphotransferase) Thymidine Kinase; Viridae; Ds-Dna Enveloped Viruses; Herpesviridae; Alphaherpesvirinae Antiviral Drug (Aciclovir) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. S. Bennett, F. Wien, J. N. Champness, T. Batuwangala, T. Rutherford, W. C. Summers, H. Sun, G. Wright, M. R. Sanderson
Structure To 1. 9 A Resolution Of A Complex With Herpes Simplex Virus Type-1 Thymidine Kinase Of A Novel, Non-Substrate Inhibitor: X-Ray Crystallographic Comparison With Binding Of Aciclovir.
Febs Lett. V. 443 121 1999
PubMed-ID: 9989588 | Reference-DOI: 10.1016/S0014-5793(98)01619-6
(for further references see the PDB file header)

Molecule 1 - PROTEIN (THYMIDINE KINASE)
	Chains	:	A, B
	EC Number	:	2.7.1.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	TK
	Expression System Strain	:	SY211
	Expression System Taxid	:	562
	Gene	:	TK
	Organism Common	:	HERPES SIMPLEX VIRUS TYPE 1
	Organism Scientific	:	HUMAN HERPESVIRUS 1
	Organism Taxid	:	10298
	Other Details	:	ACICLOVIR, ANTIVIRAL DRUG AS DEPOSITED IN 1KI5
	Strain	:	SY211
	Synonym	:	TK

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	AC2	2	Ligand/Ion	9-HYROXYETHOXYMETHYLGUANINE
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS B:58 , GLY B:59 , MET B:60 , GLY B:61 , LYS B:62 , THR B:63 , ARG B:222 , HOH B:594	BINDING SITE FOR RESIDUE SO4 B 3
2	AC2	SOFTWARE	HIS A:58 , GLY A:59 , MET A:60 , GLY A:61 , LYS A:62 , THR A:63 , ARG A:222 , HOH A:696 , HOH A:783	BINDING SITE FOR RESIDUE SO4 A 4
3	AC3	SOFTWARE	HIS A:58 , GLU A:83 , TRP A:88 , ILE A:100 , TYR A:101 , GLN A:125 , MET A:128 , ARG A:163 , TYR A:172 , ARG A:176 , ARG A:222 , GLU A:225 , HOH A:586 , HOH A:587 , HOH A:589 , HOH A:776 , HOH A:779	BINDING SITE FOR RESIDUE AC2 A 1
4	AC4	SOFTWARE	GLU B:83 , TRP B:88 , ILE B:97 , TYR B:101 , GLN B:125 , MET B:128 , ARG B:163 , TYR B:172 , ARG B:222 , HOH B:588 , HOH B:590 , HOH B:778 , HOH B:784	BINDING SITE FOR RESIDUE AC2 B 2

(no "SS Bond" information available for 2KI5)

(no "Cis Peptide Bond" information available for 2KI5)

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_KITH_HHV11_005 *	C	251	G	KITH_HHV11	---	---	A/B	C	251	G
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2KI5)

(no "Exon" information available for 2KI5)

Asymmetric/Biological 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:304
 aligned with KITH_HHV11 | P03176 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:330
                                    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       345       355       365       375
           KITH_HHV11    46 MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGEA 375
               SCOP domains d2ki5a_ A: Thymidine kina      se                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2ki5A00 A:46-375 P-loop c      ontaining nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee.......hhhhhh...------.eeee...hhhhh......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......-----...eeeeee..hhhhh.hhhhhhh......hhhhhhhhhh........eeeeee..hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh..---------------....hhh.hhhhh..hhh........hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh............hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ki5 A  46 MPTLLRVYIDGPHGMGKTTTTQLLV------DIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAG-----PPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSG---------------PRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGEA 375
                                    55        65    |    - |      85        95       105       115       125       135       145  |    155       165       175       185       195       205       215       225       235       245       255        |-         -    |  285       295       305       315       325       335       345       355       365       375
                                                   70     77                                                                    148   154                                                                                                           264             280

Chain B from PDB  Type:PROTEIN  Length:308
 aligned with KITH_HHV11 | P03176 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:330
                                    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       345       355       365       375
           KITH_HHV11    46 MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGEA 375
               SCOP domains d2ki5b_ B: Thymidine kinase                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2ki5B00 B:46-375 P-loop cont   aining nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                   CATH domains
           Pfam domains (1) ----------Herpes_TK-2ki5B01    B:56-330                                                                                                                                                                                                                                                      --------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------Herpes_TK-2ki5B02    B:56-330                                                                                                                                                                                                                                                      --------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeeee......hhhhhhhhhh..---.eeee...hhhhh......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.........-----...eeeeee..hhhhh.hhhhhhhh.....hhhhhhhhhh........eeeeee..hhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh....hhhhhhh..--------------......hhh.hhhhh..hhh........hhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ki5 B  46 MPTLLRVYIDGPHGMGKTTTTQLLVALG---DIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAG-----PPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLS--------------AGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGEA 375
                                    55        65       | - |      85        95       105       115       125       135       145  |    155       165       175       185       195       205       215       225       235       245       255       | -         -  |    285       295       305       315       325       335       345       355       365       375
                                                      73  77                                                                    148   154                                                                                                          263            278

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/Biological 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: Nucleotide and nucleoside kinases (231)

Protein domain: Thymidine kinase (34)

Herpes simplex virus type 1, different strains [TaxId: 10298] (29)

1a	d2ki5a_	A:
1b	d2ki5b_	B:

Asymmetric/Biological 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)

Herpes simplex virus type 1 (Human herpesvirus 1) (1)

1a	2ki5A00	A:46-375
1b	2ki5B00	B:46-375

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Herpes_TK (18)

Human herpesvirus 1 (strain 17) (HHV-1) (Human herpes simplex virus 1) (13)

1a	Herpes_TK-2ki5B01	B:56-330
1b	Herpes_TK-2ki5B02	B:56-330

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (KITH_HHV11 | P03176)

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:0004797	thymidine kinase activity	Catalysis of the reaction: ATP + thymidine = ADP + thymidine 5'-phosphate.
	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:0071897	DNA biosynthetic process	The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
	GO:0006230	TMP biosynthetic process	The chemical reactions and pathways resulting in the formation of TMP, ribosylthymine monophosphate.
	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.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		AC2	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ki5)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2ki5
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	KITH_HHV11 \| P03176
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.1.21
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	KITH_HHV11 \| P03176
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 2KI5)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (8, 8)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File