1U2W - 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 THE STAPHYLOCOCCUS AUREUS PI258 CADC

Authors :   J. Ye, A. Kandegedara, P. Martin, B. P. Rosen

Date :   20 Jul 04 (Deposition) - 12 Jul 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Cadmium, Lead, Repressor, Soft Metal Ion Resistance, Arsr/Smtb Family, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Ye, A. Kandegedara, P. Martin, B. P. Rosen
Crystal Structure Of The Staphylococcus Aureus Pi258 Cadc Cd(Ii)/Pb(Ii)/Zn(Ii)-Responsive Repressor
J. Bacteriol. V. 187 4214 2005
PubMed-ID: 15937183 | Reference-DOI: 10.1128/JB.187.12.4214-4221.2005

Molecule 1 - CADMIUM EFFLUX SYSTEM ACCESSORY PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PYSCM2
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CADC
	Mutation	:	YES
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Synonym	:	CADC REPRESSOR

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:101 , HIS A:103 , HIS B:114 , GLU B:117	BINDING SITE FOR RESIDUE ZN A 501
2	AC2	SOFTWARE	HIS A:114 , GLU A:117 , ASP B:101 , HIS B:103	BINDING SITE FOR RESIDUE ZN B 502
3	AC3	SOFTWARE	ASP C:101 , HIS C:103 , HIS D:114 , GLU D:117	BINDING SITE FOR RESIDUE ZN C 503

(no "SS Bond" information available for 1U2W)

Asymmetric Unit

No.	Residues
1	Gly B:92	-	Lys B:93

(no "SAP(SNP)/Variant" information available for 1U2W)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ARSR_2	PS50987	ArsR-type HTH domain profile.	CADC_STAAU	24-119	4	A:24-119 B:24-117 C:24-114 D:24-118
2	HTH_ARSR_1	PS00846	Bacterial regulatory proteins, arsR family signature.	CADC_STAAU	58-76	4	A:58-76 B:58-76 C:58-76 D:58-76

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ARSR_2	PS50987	ArsR-type HTH domain profile.	CADC_STAAU	24-119	2	A:24-119 B:24-117 - -
2	HTH_ARSR_1	PS00846	Bacterial regulatory proteins, arsR family signature.	CADC_STAAU	58-76	2	A:58-76 B:58-76 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ARSR_2	PS50987	ArsR-type HTH domain profile.	CADC_STAAU	24-119	2	- - C:24-114 D:24-118
2	HTH_ARSR_1	PS00846	Bacterial regulatory proteins, arsR family signature.	CADC_STAAU	58-76	2	- - C:58-76 D:58-76

(no "Exon" information available for 1U2W)

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:105
 aligned with CADC_STAAU | P20047 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:109
                                    20        30        40        50        60        70        80        90       100       110         
           CADC_STAAU    11 CYDEEKVNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLGDEHIRQIMMIALAHKKEVK 119
               SCOP domains -d1u2wa1 A:12-119 Cadmium efflux system accessory protein CadC                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhh.hhhhhhhhhhhhhhh..eeee----..eeee.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------HTH_ARSR_2  PDB: A:24-119 UniProt: 24-119                                                        PROSITE (1)
                PROSITE (2) -----------------------------------------------HTH_ARSR_1         ------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1u2w A  11 GYDEEKVNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFR----LALYSLGDEHIRQIMMIALAHKKEVK 119
                                    20        30        40        50        60        70        80        |-   |   100       110         
                                                                                                         89   94

Chain B from PDB  Type:PROTEIN  Length:107
 aligned with CADC_STAAU | P20047 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:107
                                    20        30        40        50        60        70        80        90       100       110       
           CADC_STAAU    11 CYDEEKVNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLGDEHIRQIMMIALAHKKE 117
               SCOP domains d1u2wb_ B: Cadmium efflux system accessory protein CadC                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhh.hhhhhhhhhhhhhhh..eeeee....eeeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------HTH_ARSR_2  PDB: B:24-117 UniProt: 24-119                                                      PROSITE (1)
                PROSITE (2) -----------------------------------------------HTH_ARSR_1         ----------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1u2w B  11 GYDEEKVNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLGDEHIRQIMMIALAHKKE 117
                                    20        30        40        50        60        70        80        90       100       110

Chain C from PDB  Type:PROTEIN  Length:98
 aligned with CADC_STAAU | P20047 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:98
                                    26        36        46        56        66        76        86        96       106        
           CADC_STAAU    17 VNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLGDEHIRQIMMIALAH 114
               SCOP domains d1u2wc_ C: Cadmium efflux system accessory protein CadC                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee..eeeeee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------HTH_ARSR_2  PDB: C:24-114 UniProt: 24-119                                                   PROSITE (1)
                PROSITE (2) -----------------------------------------HTH_ARSR_1         -------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 1u2w C  17 VNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLGDEHIRQIMMIALAH 114
                                    26        36        46        56        66        76        86        96       106

Chain D from PDB  Type:PROTEIN  Length:94
 aligned with CADC_STAAU | P20047 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:108
                                    20        30        40        50        60        70        80        90       100       110        
           CADC_STAAU    11 CYDEEKVNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLGDEHIRQIMMIALAHKKEV 118
               SCOP domains d1u2wd_ D: Cadmium efflux system accessory protein CadC                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------------------------------HTH_5-1u2wD01 D:41-81                    ------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------HTH_5-1u2wD02 D:41-81                    ------------------------------------- Pfam domains (2)
           Pfam domains (3) ------------------------------HTH_5-1u2wD03 D:41-81                    ------------------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------------HTH_5-1u2wD04 D:41-81                    ------------------------------------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhh--------------.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -------------HTH_ARSR_2  PDB: D:24-118 UniProt: 24-119                                                       PROSITE (1)
                PROSITE (2) -----------------------------------------------HTH_ARSR_1         ------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1u2w D  11 GYDEEKVNRIQGDLQTVDISGVSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLY--------------LYSLGDEHIRQIMMIALAHKKEV 118
                                    20        30        40        50        60        70        80|        -     | 100       110        
                                                                                                 81             96

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: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Winged helix DNA-binding domain (576)

Family: ArsR-like transcriptional regulators (13)

Protein domain: Cadmium efflux system accessory protein CadC (1)

Staphylococcus aureus [TaxId: 1280] (1)

1a	d1u2wa1	A:12-119
1b	d1u2wb_	B:
1c	d1u2wc_	C:
1d	d1u2wd_	D:

(no "CATH Domain" information available for 1U2W)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: HTH_5 (8)

Staphylococcus aureus (1)

1a	HTH_5-1u2wD01	D:41-81
1b	HTH_5-1u2wD02	D:41-81
1c	HTH_5-1u2wD03	D:41-81
1d	HTH_5-1u2wD04	D:41-81

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CADC_STAAU | P20047)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0046686	response to cadmium ion	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 a cadmium (Cd) ion stimulus.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
		Gly B:92 - Lys B:93	[ RasMol ]

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
	1u2w
		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
	CADC_STAAU \| P20047
		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)
	(no 'Enzyme Classificator' available)
		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
	CADC_STAAU \| P20047
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	CADC_STAAU \| P20047	:	3f72

(no "Related Entries Specified in the PDB File" available for 1U2W)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (7, 7)

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