3TTZ - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A TOPOISOMERASE ATPASE INHIBITOR

Authors :   P. A. Boriack-Sjodin, J. Read, A. E. Eakin, B. A. Sherer

Date :   15 Sep 11 (Deposition) - 16 Nov 11 (Release) - 07 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.63

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

Keywords :   Protein-Inhibitor Complex, Atp-Binding, Structure-Based Drug Design, Antimicrobial, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. A. Sherer, K. Hull, O. Green, G. Basarab, S. Hauck, P. Hill, J. T. Loch G. Mullen, S. Bist, J. Bryant, A. Boriack-Sjodin, J. Read, N. Degrace, M. Uria-Nickelsen, R. N. Illingworth, A. E. Eakin
Pyrrolamide Dna Gyrase Inhibitors: Optimization Of Antibacterial Activity And Efficacy.
Bioorg. Med. Chem. Lett. V. 21 7416 2011
PubMed-ID: 22041057 | Reference-DOI: 10.1016/J.BMCL.2011.10.010

Molecule 1 - DNA GYRASE SUBUNIT B
	Chains	:	A, B
	EC Number	:	5.99.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT73.3
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	ATPASE DOMAIN WITH LOOP DELETION, UNP RESIDUES 14-104 AND 128-233
	Gene	:	GYRB
	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 (2, 7)

No.	Name	Count	Type	Full Name
1	07N	2	Ligand/Ion	2-[(3S,4R)-4-{[(3,4-DICHLORO-5-METHYL-1H-PYRROL-2-YL)CARBONYL]AMINO}-3-FLUOROPIPERIDIN-1-YL]-1,3-THIAZOLE-5-CARBOXYLIC ACID
2	MG	5	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	07N	1	Ligand/Ion	2-[(3S,4R)-4-{[(3,4-DICHLORO-5-METHYL-1H-PYRROL-2-YL)CARBONYL]AMINO}-3-FLUOROPIPERIDIN-1-YL]-1,3-THIAZOLE-5-CARBOXYLIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	07N	1	Ligand/Ion	2-[(3S,4R)-4-{[(3,4-DICHLORO-5-METHYL-1H-PYRROL-2-YL)CARBONYL]AMINO}-3-FLUOROPIPERIDIN-1-YL]-1,3-THIAZOLE-5-CARBOXYLIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:2 , HOH A:10 , ASN A:54 , SER A:55 , GLU A:58 , ASP A:81 , ARG A:84 , GLY A:85 , ILE A:86 , PRO A:87 , ARG A:144	BINDING SITE FOR RESIDUE 07N A 1
2	AC2	SOFTWARE	HOH A:11 , HOH A:127 , HOH A:239 , HOH A:374 , HOH A:415	BINDING SITE FOR RESIDUE MG A 234
3	AC3	SOFTWARE	GLY A:208 , HIS A:228 , HOH A:324 , HOH A:327 , HOH A:340 , HOH A:351	BINDING SITE FOR RESIDUE MG A 235
4	AC4	SOFTWARE	THR A:185 , GLU A:186 , ASN B:54 , SER B:55 , GLU B:58 , ASP B:81 , ARG B:84 , GLY B:85 , ILE B:86 , PRO B:87 , ILE B:175 , HOH B:239	BINDING SITE FOR RESIDUE 07N B 2
5	AC5	SOFTWARE	ASN B:54 , HOH B:316 , HOH B:331 , HOH B:361 , HOH B:371 , HOH B:398	BINDING SITE FOR RESIDUE MG B 1
6	AC6	SOFTWARE	HOH A:244 , HOH A:273 , HOH B:107 , HOH B:120	BINDING SITE FOR RESIDUE MG B 234
7	AC7	SOFTWARE	GLY B:208 , HIS B:228 , HOH B:273 , HOH B:302 , HOH B:314 , HOH B:352	BINDING SITE FOR RESIDUE MG B 235

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

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

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

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

(no "Exon" information available for 3TTZ)

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:194
 aligned with GYRB_STAAU | P0A0K8 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:217
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       
           GYRB_STAAU    14 YGAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
               SCOP domains d3ttza_ A: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeeeehhheeeeee...............hhhhhhhh-----------------------hhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ttz A  14 YGAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILT-----------------------SSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
                                    23        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:185
 aligned with GYRB_STAAU | P0A0K8 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:211
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229 
           GYRB_STAAU    20 QVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
               SCOP domains d3ttzb_ B: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeeeehhheeeeee..........---..hhhhhhhh-----------------------.hhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ttz B  20 QVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQ---GRPAVEVILT-----------------------SSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
                                    29        39        49        59        69        79        89 |   |  99    |    -         -       129       139       149       159       169       179       189       199       209       219       229 
                                                                                                  91  95      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 '\|'

(no "CATH Domain" information available for 3TTZ)

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

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.

Asymmetric 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
		07N	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ttz)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 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
	3ttz
		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
	GYRB_STAAU \| P0A0K8
		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)
	5.99.1.3
		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
	GYRB_STAAU \| P0A0K8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

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