3G75 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS GYRASE B CO-COMPLEXED WITH 4-METHYL-5-[3-(METHYLSULFANYL)-1H-PYRAZOL-5-YL]-2-THIOPHEN-2-YL-1,3-THIAZOLE INHIBITOR

Authors :   Y. Wei, P. Charifson

Date :   09 Feb 09 (Deposition) - 09 Feb 10 (Release) - 03 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Antibiotic Resistance, Isomerase, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. M. Ronkin, M. Badia, S. Bellon, A. L. Grillot, C. H. Gross, T. H. Grossman, N. Mani, J. D. Parsons, D. Stamos, M. Trudeau, Y. Wei, P. S. Charifson
Discovery Of Pyrazolthiazoles As Novel And Potent Inhibitor Of Bacterial Gyrase.
Bioorg. Med. Chem. Lett. V. 20 2828 2010
PubMed-ID: 20356737 | Reference-DOI: 10.1016/J.BMCL.2010.03.052

Molecule 1 - DNA GYRASE SUBUNIT B
	Chains	:	A, B
	EC Number	:	5.99.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 24-230
	Gene	:	GYRB
	Mutation	:	YES
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	B48	2	Ligand/Ion	4-METHYL-5-[3-(METHYLSULFANYL)-1H-PYRAZOL-5-YL]-2-THIOPHEN-2-YL-1,3-THIAZOLE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	B48	1	Ligand/Ion	4-METHYL-5-[3-(METHYLSULFANYL)-1H-PYRAZOL-5-YL]-2-THIOPHEN-2-YL-1,3-THIAZOLE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	B48	1	Ligand/Ion	4-METHYL-5-[3-(METHYLSULFANYL)-1H-PYRAZOL-5-YL]-2-THIOPHEN-2-YL-1,3-THIAZOLE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE B:51 , SER B:55 , GLU B:58 , ASP B:81 , ARG B:84 , PRO B:87 , HOH B:123 , HOH B:337	BINDING SITE FOR RESIDUE B48 B 1
2	AC2	SOFTWARE	SER A:55 , GLU A:58 , ASP A:81 , ARG A:84 , ILE A:86 , ILE A:175 , HOH A:348	BINDING SITE FOR RESIDUE B48 A 2

(no "SS Bond" information available for 3G75)

(no "Cis Peptide Bond" information available for 3G75)

(no "SAP(SNP)/Variant" information available for 3G75)

(no "PROSITE Motif" information available for 3G75)

(no "Exon" information available for 3G75)

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:184
 aligned with GYRB_STAAU | P0A0K8 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:207
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       
           GYRB_STAAU    24 GLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
               SCOP domains d3g75a_ A: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains 3g75A00 A:24-230  [code=3.30.565.10, no name defined]                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh...hhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhh.eeeee...............hhhhhhhh-----------------------.hhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g75 A  24 GLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILT-----------------------SSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
                                    33        43        53        63        73        83        93       103|        -         -    |  133       143       153       163       173       183       193       203       213       223       
                                                                                                          104                     128

Chain B from PDB  Type:PROTEIN  Length:184
 aligned with GYRB_STAAU | P0A0K8 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:207
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       
           GYRB_STAAU    24 GLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
               SCOP domains d3g75b_ B: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains 3g75B00 B:24-230  [code=3.30.565.10, no name defined]                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhh.eeeee...............hhhhhhhh-----------------------.hhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g75 B  24 GLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILT-----------------------SSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
                                    33        43        53        63        73        83        93       103|        -         -    |  133       143       153       163       173       183       193       203       213       223       
                                                                                                          104                     128

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Heat Shock Protein 90 (209)

Homologous Superfamily: [code=3.30.565.10, no name defined] (205)

Staphylococcus aureus. Organism_taxid: 1280. (2)

1a	3g75A00	A:24-230
1b	3g75B00	B:24-230

(no "Pfam Domain" information available for 3G75)

Asymmetric Unit(hide GO term definitions)

Chain A,B (GYRB_STAAU | P0A0K8)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003916	DNA topoisomerase activity	Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA.
	GO:0003918	DNA topoisomerase type II (ATP-hydrolyzing) activity	Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
biological process
	GO:0006265	DNA topological change	The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.
	GO:0006261	DNA-dependent DNA replication	A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
	GO:0046677	response to antibiotic	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 an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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Biological Units
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	3g75
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	5.99.1.3
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3g7b	STAPHYLOCOCCUS AUREUS GYRASE B CO-COMPLEX WITH INHIBITOR
3g7e	CRYSTAL STRUCTURE OF E. COLI GYRASE B CO-COMPLEXED WITH INHIBITOR

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Gene Ontology (13, 13)

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